gromacs →
2020.1-1 →
armhf → 2020-04-17 19:52:58
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| gromacs 2020.1-1 (armhf) Fri, 17 Apr 2020 06:54:08 +0000 |
+==============================================================================+
Package: gromacs
Version: 2020.1-1
Source Version: 2020.1-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-576d08da-9072-4961-b4fb-a573fabb96a6' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 27s (900 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 29.2 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gromacs 2020.1-1 (dsc) [2581 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gromacs 2020.1-1 (tar) [29.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main gromacs 2020.1-1 (diff) [37.1 kB]
Fetched 29.2 MB in 10s (3062 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-QwOYEj/gromacs-2020.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-QwOYEj' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-MCsUYP/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-MCsUYP/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-MCsUYP/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2647 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12225 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
Filtered Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-MCsUYP/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Sources [584 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ Packages [659 B]
Fetched 2576 B in 1s (3455 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism distro-info-data
dwz file gettext gettext-base gfortran gfortran-9 groff-base hwloc-nox
ibverbs-providers intltool-debian libarchive-zip-perl libarchive13
libblas-dev libblas3 libboost-dev libboost1.67-dev libbrotli1 libbsd0
libcbor0 libcroco3 libcurl4 libdebhelper-perl libedit2 libelf1
libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfftw3-bin
libfftw3-dev libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0
libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev
libibverbs1 libicu63 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libltdl-dev libltdl7 libmagic-mgc
libmagic1 libmpdec2 libmpich-dev libmpich12 libncurses6 libnghttp2-14
libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev
libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2
libprocps8 libpsl5 libpthread-stubs0-dev libpython3-stdlib
libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2
libssh2-1 libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0
libuv1 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1
libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release
m4 man-db mime-support mpich ocl-icd-libopencl1 openmpi-bin openmpi-common
openssh-client po-debconf procps python3 python3-minimal python3.8
python3.8-minimal sensible-utils x11proto-core-dev x11proto-dev
xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-9-doc libcoarrays-dev groff lrzip
liblapack-doc libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-contract1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libfftw3-doc krb5-doc krb5-user libtool-doc openmpi-doc pciutils gcj-jdk
libx11-doc libxcb-doc m4-doc apparmor less www-browser mpich-doc opencl-icd
keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc
python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev
publicsuffix xauth libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism distro-info-data
dwz file gettext gettext-base gfortran gfortran-9 groff-base hwloc-nox
ibverbs-providers intltool-debian libarchive-zip-perl libarchive13
libblas-dev libblas3 libboost-dev libboost1.67-dev libbrotli1 libbsd0
libcbor0 libcroco3 libcurl4 libdebhelper-perl libedit2 libelf1
libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfftw3-bin
libfftw3-dev libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0
libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev
libibverbs1 libicu63 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libltdl-dev libltdl7 libmagic-mgc
libmagic1 libmpdec2 libmpich-dev libmpich12 libncurses6 libnghttp2-14
libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev
libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2
libprocps8 libpsl5 libpthread-stubs0-dev libpython3-stdlib
libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2
libssh2-1 libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0
libuv1 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1
libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release
m4 man-db mime-support mpich ocl-icd-libopencl1 openmpi-bin openmpi-common
openssh-client po-debconf procps python3 python3-minimal python3.8
python3.8-minimal sbuild-build-depends-gromacs-dummy sensible-utils
x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
0 upgraded, 136 newly installed, 0 to remove and 3 not upgraded.
Need to get 68.3 MB of archives.
After this operation, 353 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MCsUYP/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1f-1 [1272 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.2-1 [744 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.2-1 [1628 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-3 [37.6 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-3 [68.1 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.2-1 [1597 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.2-1 [410 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-3 [20.8 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-4 [59.8 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-4 [238 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-1 [79.2 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libfido2-1 armhf 1.3.1-1 [42.2 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7 [61.4 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7 [112 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7 [320 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7 [135 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.2p1-4 [781 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.16.3-1 [1628 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-4 [592 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.0-2 [292 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1 [53.9 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.68.0-1 [286 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.9-1 [133 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.34.2-1 [114 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.16.3-1 [2648 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.10 [184 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.7.0-1 [23.8 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.7.0-1 [14.8 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.1-1 [1157 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.10 [1003 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf distro-info-data all 0.43 [6540 B]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10-20200324-1+rpi1 [230 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-10+rpi1 [278 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-10+rpi1 [8107 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.2.0+dfsg-3 [113 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf hwloc-nox armhf 2.2.0+dfsg-3 [149 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 28.0-1+b1 [47.9 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 28.0-1+b1 [24.5 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-17 [8389 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b11 [4464 B]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.11-stable-1 [165 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.11-stable-1 [124 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.11-stable-1 [98.7 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.11-stable-1 [54.7 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.11-stable-1 [59.7 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.11-stable-1 [279 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-14 [388 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-14 [159 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.2.0+dfsg-3 [174 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 440.64-1 [25.1 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-3 [35.9 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.2.0+dfsg-3 [19.0 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 28.0-1+b1 [167 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-2 [1602 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-2 [2981 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libmpich12 armhf 3.4~a2+really3.3.2-1 [1057 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf mpich armhf 3.4~a2+really3.3.2-1 [335 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libmpich-dev armhf 3.4~a2+really3.3.2-1 [1528 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.5-1 [377 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.0.2-5+rpi1 [1679 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.0.2-5+rpi1 [168 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.0.2-5+rpi1 [185 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.0.2-5+rpi1 [905 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2019.2-1 [593 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf x11proto-core-dev all 2019.2-1 [3256 B]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.14-2 [173 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.6.9-2 [766 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 68.3 MB in 21s (3243 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12225 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
Selecting previously unselected package libtinfo5:armhf.
Preparing to unpack .../01-libtinfo5_6.2-1_armhf.deb ...
Unpacking libtinfo5:armhf (6.2-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../02-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../03-libuchardet0_0.0.6-3_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.6-3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../04-groff-base_1.22.4-4_armhf.deb ...
Unpacking groff-base (1.22.4-4) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../05-libpipeline1_1.5.2-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.2-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../06-man-db_2.9.1-1_armhf.deb ...
Unpacking man-db (2.9.1-1) ...
Selecting previously unselected package libssl1.1:armhf.
Preparing to unpack .../07-libssl1.1_1.1.1f-1_armhf.deb ...
Unpacking libssl1.1:armhf (1.1.1f-1) ...
Selecting previously unselected package libpython3.8-minimal:armhf.
Preparing to unpack .../08-libpython3.8-minimal_3.8.2-1_armhf.deb ...
Unpacking libpython3.8-minimal:armhf (3.8.2-1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../09-libexpat1_2.2.9-1_armhf.deb ...
Unpacking libexpat1:armhf (2.2.9-1) ...
Selecting previously unselected package python3.8-minimal.
Preparing to unpack .../10-python3.8-minimal_3.8.2-1_armhf.deb ...
Unpacking python3.8-minimal (3.8.2-1) ...
Setting up libssl1.1:armhf (1.1.1f-1) ...
Setting up libpython3.8-minimal:armhf (3.8.2-1) ...
Setting up libexpat1:armhf (2.2.9-1) ...
Setting up python3.8-minimal (3.8.2-1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13187 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.8.2-3_armhf.deb ...
Unpacking python3-minimal (3.8.2-3) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../1-mime-support_3.64_all.deb ...
Unpacking mime-support (3.64) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../2-libmpdec2_2.4.2-3_armhf.deb ...
Unpacking libmpdec2:armhf (2.4.2-3) ...
Selecting previously unselected package libpython3.8-stdlib:armhf.
Preparing to unpack .../3-libpython3.8-stdlib_3.8.2-1_armhf.deb ...
Unpacking libpython3.8-stdlib:armhf (3.8.2-1) ...
Selecting previously unselected package python3.8.
Preparing to unpack .../4-python3.8_3.8.2-1_armhf.deb ...
Unpacking python3.8 (3.8.2-1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../5-libpython3-stdlib_3.8.2-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.8.2-3) ...
Setting up python3-minimal (3.8.2-3) ...
Selecting previously unselected package python3.
(Reading database ... 13589 files and directories currently installed.)
Preparing to unpack .../000-python3_3.8.2-3_armhf.deb ...
Unpacking python3 (3.8.2-3) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../001-libncurses6_6.2-1_armhf.deb ...
Unpacking libncurses6:armhf (6.2-1) ...
Selecting previously unselected package libprocps8:armhf.
Preparing to unpack .../002-libprocps8_2%3a3.3.16-4_armhf.deb ...
Unpacking libprocps8:armhf (2:3.3.16-4) ...
Selecting previously unselected package procps.
Preparing to unpack .../003-procps_2%3a3.3.16-4_armhf.deb ...
Unpacking procps (2:3.3.16-4) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../004-sensible-utils_0.0.12+nmu1_all.deb ...
Unpacking sensible-utils (0.0.12+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../005-libmagic-mgc_1%3a5.38-4_armhf.deb ...
Unpacking libmagic-mgc (1:5.38-4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../006-libmagic1_1%3a5.38-4_armhf.deb ...
Unpacking libmagic1:armhf (1:5.38-4) ...
Selecting previously unselected package file.
Preparing to unpack .../007-file_1%3a5.38-4_armhf.deb ...
Unpacking file (1:5.38-4) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../008-gettext-base_0.19.8.1-10_armhf.deb ...
Unpacking gettext-base (0.19.8.1-10) ...
Selecting previously unselected package libedit2:armhf.
Preparing to unpack .../009-libedit2_3.1-20191231-1_armhf.deb ...
Unpacking libedit2:armhf (3.1-20191231-1) ...
Selecting previously unselected package libcbor0:armhf.
Preparing to unpack .../010-libcbor0_0.5.0+dfsg-2_armhf.deb ...
Unpacking libcbor0:armhf (0.5.0+dfsg-2) ...
Selecting previously unselected package libfido2-1:armhf.
Preparing to unpack .../011-libfido2-1_1.3.1-1_armhf.deb ...
Unpacking libfido2-1:armhf (1.3.1-1) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../012-libkrb5support0_1.17-7_armhf.deb ...
Unpacking libkrb5support0:armhf (1.17-7) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../013-libk5crypto3_1.17-7_armhf.deb ...
Unpacking libk5crypto3:armhf (1.17-7) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../014-libkeyutils1_1.6.1-2_armhf.deb ...
Unpacking libkeyutils1:armhf (1.6.1-2) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../015-libkrb5-3_1.17-7_armhf.deb ...
Unpacking libkrb5-3:armhf (1.17-7) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../016-libgssapi-krb5-2_1.17-7_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.17-7) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../017-openssh-client_1%3a8.2p1-4_armhf.deb ...
Unpacking openssh-client (1:8.2p1-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../018-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../019-m4_1.4.18-4_armhf.deb ...
Unpacking m4 (1.4.18-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../020-autoconf_2.69-11.1_all.deb ...
Unpacking autoconf (2.69-11.1) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../021-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../022-automake_1%3a1.16.2-1_all.deb ...
Unpacking automake (1:1.16.2-1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../023-autopoint_0.19.8.1-10_all.deb ...
Unpacking autopoint (0.19.8.1-10) ...
Selecting previously unselected package chrpath.
Preparing to unpack .../024-chrpath_0.16-2_armhf.deb ...
Unpacking chrpath (0.16-2) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../025-cmake-data_3.16.3-1_all.deb ...
Unpacking cmake-data (3.16.3-1) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../026-libicu63_63.2-3_armhf.deb ...
Unpacking libicu63:armhf (63.2-3) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../027-libxml2_2.9.10+dfsg-4_armhf.deb ...
Unpacking libxml2:armhf (2.9.10+dfsg-4) ...
Selecting previously unselected package libarchive13:armhf.
Preparing to unpack .../028-libarchive13_3.4.0-2_armhf.deb ...
Unpacking libarchive13:armhf (3.4.0-2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../029-libbrotli1_1.0.7-6_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.7-6) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../030-libnghttp2-14_1.40.0-1+b2_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.40.0-1+b2) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../031-libpsl5_0.21.0-1_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../032-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../033-libssh2-1_1.8.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../034-libcurl4_7.68.0-1_armhf.deb ...
Unpacking libcurl4:armhf (7.68.0-1) ...
Selecting previously unselected package libjsoncpp1:armhf.
Preparing to unpack .../035-libjsoncpp1_1.7.4-3.1_armhf.deb ...
Unpacking libjsoncpp1:armhf (1.7.4-3.1) ...
Selecting previously unselected package librhash0:armhf.
Preparing to unpack .../036-librhash0_1.3.9-1_armhf.deb ...
Unpacking librhash0:armhf (1.3.9-1) ...
Selecting previously unselected package libuv1:armhf.
Preparing to unpack .../037-libuv1_1.34.2-1_armhf.deb ...
Unpacking libuv1:armhf (1.34.2-1) ...
Selecting previously unselected package cmake.
Preparing to unpack .../038-cmake_3.16.3-1_armhf.deb ...
Unpacking cmake (3.16.3-1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../039-libtool_2.4.6-14_all.deb ...
Unpacking libtool (2.4.6-14) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../040-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../041-libdebhelper-perl_12.10_all.deb ...
Unpacking libdebhelper-perl (12.10) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../042-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../043-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../044-libfile-stripnondeterminism-perl_1.7.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.7.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../045-dh-strip-nondeterminism_1.7.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.7.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../046-libelf1_0.176-1.1_armhf.deb ...
Unpacking libelf1:armhf (0.176-1.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../047-dwz_0.13-5_armhf.deb ...
Unpacking dwz (0.13-5) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../048-libglib2.0-0_2.64.1-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.64.1-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../049-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../050-gettext_0.19.8.1-10_armhf.deb ...
Unpacking gettext (0.19.8.1-10) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../051-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../052-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../053-debhelper_12.10_all.deb ...
Unpacking debhelper (12.10) ...
Selecting previously unselected package distro-info-data.
Preparing to unpack .../054-distro-info-data_0.43_all.deb ...
Unpacking distro-info-data (0.43) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../055-libgfortran5_10-20200324-1+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (10-20200324-1+rpi1) ...
Selecting previously unselected package libgfortran-9-dev:armhf.
Preparing to unpack .../056-libgfortran-9-dev_9.3.0-10+rpi1_armhf.deb ...
Unpacking libgfortran-9-dev:armhf (9.3.0-10+rpi1) ...
Selecting previously unselected package gfortran-9.
Preparing to unpack .../057-gfortran-9_9.3.0-10+rpi1_armhf.deb ...
Unpacking gfortran-9 (9.3.0-10+rpi1) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../058-gfortran_4%3a9.2.1-3.1+rpi1_armhf.deb ...
Unpacking gfortran (4:9.2.1-3.1+rpi1) ...
Selecting previously unselected package libhwloc15:armhf.
Preparing to unpack .../059-libhwloc15_2.2.0+dfsg-3_armhf.deb ...
Unpacking libhwloc15:armhf (2.2.0+dfsg-3) ...
Selecting previously unselected package hwloc-nox.
Preparing to unpack .../060-hwloc-nox_2.2.0+dfsg-3_armhf.deb ...
Unpacking hwloc-nox (2.2.0+dfsg-3) ...
Selecting previously unselected package libnl-3-200:armhf.
Preparing to unpack .../061-libnl-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libnl-route-3-200:armhf.
Preparing to unpack .../062-libnl-route-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-route-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libibverbs1:armhf.
Preparing to unpack .../063-libibverbs1_28.0-1+b1_armhf.deb ...
Unpacking libibverbs1:armhf (28.0-1+b1) ...
Selecting previously unselected package ibverbs-providers:armhf.
Preparing to unpack .../064-ibverbs-providers_28.0-1+b1_armhf.deb ...
Unpacking ibverbs-providers:armhf (28.0-1+b1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../065-libblas3_3.9.0-2_armhf.deb ...
Unpacking libblas3:armhf (3.9.0-2) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../066-libblas-dev_3.9.0-2_armhf.deb ...
Unpacking libblas-dev:armhf (3.9.0-2) ...
Selecting previously unselected package libboost1.67-dev:armhf.
Preparing to unpack .../067-libboost1.67-dev_1.67.0-17_armhf.deb ...
Unpacking libboost1.67-dev:armhf (1.67.0-17) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../068-libboost-dev_1.67.0.2+b11_armhf.deb ...
Unpacking libboost-dev:armhf (1.67.0.2+b11) ...
Selecting previously unselected package libevent-2.1-7:armhf.
Preparing to unpack .../069-libevent-2.1-7_2.1.11-stable-1_armhf.deb ...
Unpacking libevent-2.1-7:armhf (2.1.11-stable-1) ...
Selecting previously unselected package libevent-core-2.1-7:armhf.
Preparing to unpack .../070-libevent-core-2.1-7_2.1.11-stable-1_armhf.deb ...
Unpacking libevent-core-2.1-7:armhf (2.1.11-stable-1) ...
Selecting previously unselected package libevent-extra-2.1-7:armhf.
Preparing to unpack .../071-libevent-extra-2.1-7_2.1.11-stable-1_armhf.deb ...
Unpacking libevent-extra-2.1-7:armhf (2.1.11-stable-1) ...
Selecting previously unselected package libevent-pthreads-2.1-7:armhf.
Preparing to unpack .../072-libevent-pthreads-2.1-7_2.1.11-stable-1_armhf.deb ...
Unpacking libevent-pthreads-2.1-7:armhf (2.1.11-stable-1) ...
Selecting previously unselected package libevent-openssl-2.1-7:armhf.
Preparing to unpack .../073-libevent-openssl-2.1-7_2.1.11-stable-1_armhf.deb ...
Unpacking libevent-openssl-2.1-7:armhf (2.1.11-stable-1) ...
Selecting previously unselected package libevent-dev.
Preparing to unpack .../074-libevent-dev_2.1.11-stable-1_armhf.deb ...
Unpacking libevent-dev (2.1.11-stable-1) ...
Selecting previously unselected package libfftw3-double3:armhf.
Preparing to unpack .../075-libfftw3-double3_3.3.8-2_armhf.deb ...
Unpacking libfftw3-double3:armhf (3.3.8-2) ...
Selecting previously unselected package libfftw3-single3:armhf.
Preparing to unpack .../076-libfftw3-single3_3.3.8-2_armhf.deb ...
Unpacking libfftw3-single3:armhf (3.3.8-2) ...
Selecting previously unselected package libfftw3-bin.
Preparing to unpack .../077-libfftw3-bin_3.3.8-2_armhf.deb ...
Unpacking libfftw3-bin (3.3.8-2) ...
Selecting previously unselected package libfftw3-dev:armhf.
Preparing to unpack .../078-libfftw3-dev_3.3.8-2_armhf.deb ...
Unpacking libfftw3-dev:armhf (3.3.8-2) ...
Selecting previously unselected package libnuma1:armhf.
Preparing to unpack .../079-libnuma1_2.0.12-1_armhf.deb ...
Unpacking libnuma1:armhf (2.0.12-1) ...
Selecting previously unselected package libnuma-dev:armhf.
Preparing to unpack .../080-libnuma-dev_2.0.12-1_armhf.deb ...
Unpacking libnuma-dev:armhf (2.0.12-1) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../081-libltdl7_2.4.6-14_armhf.deb ...
Unpacking libltdl7:armhf (2.4.6-14) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../082-libltdl-dev_2.4.6-14_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.6-14) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../083-libhwloc-dev_2.2.0+dfsg-3_armhf.deb ...
Unpacking libhwloc-dev:armhf (2.2.0+dfsg-3) ...
Selecting previously unselected package libpciaccess0:armhf.
Preparing to unpack .../084-libpciaccess0_0.14-1_armhf.deb ...
Unpacking libpciaccess0:armhf (0.14-1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../085-libxau6_1%3a1.0.8-1+b2_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../086-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../087-libxcb1_1.14-2_armhf.deb ...
Unpacking libxcb1:armhf (1.14-2) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../088-libx11-data_2%3a1.6.9-2_all.deb ...
Unpacking libx11-data (2:1.6.9-2) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../089-libx11-6_2%3a1.6.9-2_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.9-2) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../090-libxext6_2%3a1.3.3-1+b2_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1+b2) ...
Selecting previously unselected package libxnvctrl0:armhf.
Preparing to unpack .../091-libxnvctrl0_440.64-1_armhf.deb ...
Unpacking libxnvctrl0:armhf (440.64-1) ...
Selecting previously unselected package ocl-icd-libopencl1:armhf.
Preparing to unpack .../092-ocl-icd-libopencl1_2.2.12-3_armhf.deb ...
Unpacking ocl-icd-libopencl1:armhf (2.2.12-3) ...
Selecting previously unselected package libhwloc-plugins:armhf.
Preparing to unpack .../093-libhwloc-plugins_2.2.0+dfsg-3_armhf.deb ...
Unpacking libhwloc-plugins:armhf (2.2.0+dfsg-3) ...
Selecting previously unselected package libnl-3-dev:armhf.
Preparing to unpack .../094-libnl-3-dev_3.4.0-1_armhf.deb ...
Unpacking libnl-3-dev:armhf (3.4.0-1) ...
Selecting previously unselected package libnl-route-3-dev:armhf.
Preparing to unpack .../095-libnl-route-3-dev_3.4.0-1_armhf.deb ...
Unpacking libnl-route-3-dev:armhf (3.4.0-1) ...
Selecting previously unselected package libibverbs-dev:armhf.
Preparing to unpack .../096-libibverbs-dev_28.0-1+b1_armhf.deb ...
Unpacking libibverbs-dev:armhf (28.0-1+b1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../097-liblapack3_3.9.0-2_armhf.deb ...
Unpacking liblapack3:armhf (3.9.0-2) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../098-liblapack-dev_3.9.0-2_armhf.deb ...
Unpacking liblapack-dev:armhf (3.9.0-2) ...
Selecting previously unselected package libmpich12:armhf.
Preparing to unpack .../099-libmpich12_3.4~a2+really3.3.2-1_armhf.deb ...
Unpacking libmpich12:armhf (3.4~a2+really3.3.2-1) ...
Selecting previously unselected package mpich.
Preparing to unpack .../100-mpich_3.4~a2+really3.3.2-1_armhf.deb ...
Unpacking mpich (3.4~a2+really3.3.2-1) ...
Selecting previously unselected package libmpich-dev:armhf.
Preparing to unpack .../101-libmpich-dev_3.4~a2+really3.3.2-1_armhf.deb ...
Unpacking libmpich-dev:armhf (3.4~a2+really3.3.2-1) ...
Selecting previously unselected package libpmix2:armhf.
Preparing to unpack .../102-libpmix2_3.1.5-1_armhf.deb ...
Unpacking libpmix2:armhf (3.1.5-1) ...
Selecting previously unselected package libopenmpi3:armhf.
Preparing to unpack .../103-libopenmpi3_4.0.2-5+rpi1_armhf.deb ...
Unpacking libopenmpi3:armhf (4.0.2-5+rpi1) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../104-openmpi-common_4.0.2-5+rpi1_all.deb ...
Unpacking openmpi-common (4.0.2-5+rpi1) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../105-openmpi-bin_4.0.2-5+rpi1_armhf.deb ...
Unpacking openmpi-bin (4.0.2-5+rpi1) ...
Selecting previously unselected package libopenmpi-dev:armhf.
Preparing to unpack .../106-libopenmpi-dev_4.0.2-5+rpi1_armhf.deb ...
Unpacking libopenmpi-dev:armhf (4.0.2-5+rpi1) ...
Selecting previously unselected package libpthread-stubs0-dev:armhf.
Preparing to unpack .../107-libpthread-stubs0-dev_0.4-1_armhf.deb ...
Unpacking libpthread-stubs0-dev:armhf (0.4-1) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../108-xorg-sgml-doctools_1%3a1.11-1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1) ...
Selecting previously unselected package x11proto-dev.
Preparing to unpack .../109-x11proto-dev_2019.2-1_all.deb ...
Unpacking x11proto-dev (2019.2-1) ...
Selecting previously unselected package x11proto-core-dev.
Preparing to unpack .../110-x11proto-core-dev_2019.2-1_all.deb ...
Unpacking x11proto-core-dev (2019.2-1) ...
Selecting previously unselected package libxau-dev:armhf.
Preparing to unpack .../111-libxau-dev_1%3a1.0.8-1+b2_armhf.deb ...
Unpacking libxau-dev:armhf (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp-dev:armhf.
Preparing to unpack .../112-libxdmcp-dev_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp-dev:armhf (1:1.1.2-3) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../113-xtrans-dev_1.4.0-1_all.deb ...
Unpacking xtrans-dev (1.4.0-1) ...
Selecting previously unselected package libxcb1-dev:armhf.
Preparing to unpack .../114-libxcb1-dev_1.14-2_armhf.deb ...
Unpacking libxcb1-dev:armhf (1.14-2) ...
Selecting previously unselected package libx11-dev:armhf.
Preparing to unpack .../115-libx11-dev_2%3a1.6.9-2_armhf.deb ...
Unpacking libx11-dev:armhf (2:1.6.9-2) ...
Selecting previously unselected package lsb-release.
Preparing to unpack .../116-lsb-release_11.1.0+rpi1_all.deb ...
Unpacking lsb-release (11.1.0+rpi1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../117-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-gromacs-dummy.
Preparing to unpack .../118-sbuild-build-depends-gromacs-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Setting up libboost1.67-dev:armhf (1.67.0-17) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1) ...
Setting up libfftw3-single3:armhf (3.3.8-2) ...
Setting up mime-support (3.64) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.1-1) ...
No schema files found: doing nothing.
Setting up distro-info-data (0.43) ...
Setting up libdebhelper-perl (12.10) ...
Setting up libbrotli1:armhf (1.0.7-6) ...
Setting up libcbor0:armhf (0.5.0+dfsg-2) ...
Setting up libnghttp2-14:armhf (1.40.0-1+b2) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-4) ...
Setting up libpthread-stubs0-dev:armhf (0.4-1) ...
Setting up libicu63:armhf (63.2-3) ...
Setting up libkrb5support0:armhf (1.17-7) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.34.2-1) ...
Setting up libx11-data (2:1.6.9-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libhwloc15:armhf (2.2.0+dfsg-3) ...
Setting up libevent-core-2.1-7:armhf (2.1.11-stable-1) ...
Setting up libevent-2.1-7:armhf (2.1.11-stable-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libk5crypto3:armhf (1.17-7) ...
Setting up libltdl7:armhf (2.4.6-14) ...
Setting up libfftw3-double3:armhf (3.3.8-2) ...
Setting up libgfortran5:armhf (10-20200324-1+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libnuma1:armhf (2.0.12-1) ...
Setting up libmpich12:armhf (3.4~a2+really3.3.2-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-3) ...
Setting up librhash0:armhf (1.3.9-1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up openmpi-common (4.0.2-5+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up cmake-data (3.16.3-1) ...
Setting up libkrb5-3:armhf (1.17-7) ...
Setting up libboost-dev:armhf (1.67.0.2+b11) ...
Setting up libmpdec2:armhf (2.4.2-3) ...
Setting up libpython3.8-stdlib:armhf (3.8.2-1) ...
Setting up libfido2-1:armhf (1.3.1-1) ...
Setting up python3.8 (3.8.2-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-4) ...
Setting up chrpath (0.16-2) ...
Setting up libprocps8:armhf (2:3.3.16-4) ...
Setting up libblas-dev:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libjsoncpp1:armhf (1.7.4-3.1) ...
Setting up libpython3-stdlib:armhf (3.8.2-3) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.11-stable-1) ...
Setting up x11proto-dev (2019.2-1) ...
Setting up libfile-stripnondeterminism-perl (1.7.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.11-stable-1) ...
Setting up liblapack3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.14-2) ...
Setting up libxau-dev:armhf (1:1.0.8-1+b2) ...
Setting up libtool (2.4.6-14) ...
Setting up libarchive13:armhf (3.4.0-2) ...
Setting up libfftw3-bin (3.3.8-2) ...
Setting up libedit2:armhf (3.1-20191231-1) ...
Setting up hwloc-nox (2.2.0+dfsg-3) ...
Setting up libgfortran-9-dev:armhf (9.3.0-10+rpi1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.11-stable-1) ...
Setting up m4 (1.4.18-4) ...
Setting up python3 (3.8.2-3) ...
Setting up libnuma-dev:armhf (2.0.12-1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up x11proto-core-dev (2019.2-1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libevent-dev (2.1.11-stable-1) ...
Setting up liblapack-dev:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-7) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.7.0-1) ...
Setting up dwz (0.13-5) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-4) ...
Setting up procps (2:3.3.16-4) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libcurl4:armhf (7.68.0-1) ...
Setting up libx11-6:armhf (2:1.6.9-2) ...
Setting up lsb-release (11.1.0+rpi1) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up automake (1:1.16.2-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (28.0-1+b1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libxcb1-dev:armhf (1.14-2) ...
Setting up gfortran-9 (9.3.0-10+rpi1) ...
Setting up ibverbs-providers:armhf (28.0-1+b1) ...
Setting up mpich (3.4~a2+really3.3.2-1) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up openssh-client (1:8.2p1-4) ...
Setting up libx11-dev:armhf (2:1.6.9-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:9.2.1-3.1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libxnvctrl0:armhf (440.64-1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-14) ...
Setting up libmpich-dev:armhf (3.4~a2+really3.3.2-1) ...
update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up cmake (3.16.3-1) ...
Setting up libhwloc-dev:armhf (2.2.0+dfsg-3) ...
Setting up po-debconf (1.0.21) ...
Setting up libibverbs-dev:armhf (28.0-1+b1) ...
Setting up libhwloc-plugins:armhf (2.2.0+dfsg-3) ...
Setting up libpmix2:armhf (3.1.5-1) ...
Setting up libopenmpi3:armhf (4.0.2-5+rpi1) ...
Setting up openmpi-bin (4.0.2-5+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.0.2-5+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up debhelper (12.10) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.30-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-10+rpi1 gcc-9_9.3.0-10+rpi1 libc6-dev_2.30-4+rpi1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200324-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 chrpath_0.16-2 cmake_3.16.3-1 cmake-data_3.16.3-1 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-10+rpi1 dash_0.5.10.2-7 debconf_1.5.73 debhelper_12.10 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.7.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 distro-info-data_0.43 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-10+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200324-1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-5 gcc-8-base_8.4.0-1+rpi1 gcc-9_9.3.0-10+rpi1 gcc-9-base_9.3.0-10+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.3.0-10+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 hwloc-nox_2.2.0+dfsg-3 ibverbs-providers_28.0-1+b1 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libarchive13_3.4.0-2 libasan5_9.3.0-10+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200324-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b11 libboost1.67-dev_1.67.0-17 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4+rpi1 libc-dev-bin_2.30-4+rpi1 libc6_2.30-4+rpi1 libc6-dev_2.30-4+rpi1 libcap-ng0_0.7.9-2.1+b1 libcbor0_0.5.0+dfsg-2 libcc1-0_10-20200324-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libcurl4_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.10 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libevent-2.1-7_2.1.11-stable-1 libevent-core-2.1-7_2.1.11-stable-1 libevent-dev_2.1.11-stable-1 libevent-extra-2.1-7_2.1.11-stable-1 libevent-openssl-2.1-7_2.1.11-stable-1 libevent-pthreads-2.1-7_2.1.11-stable-1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.3.1-1 libfile-stripnondeterminism-perl_1.7.0-1 libgcc-9-dev_9.3.0-10+rpi1 libgcc-s1_10-20200324-1+rpi1 libgcc1_1:10-20200324-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-10+rpi1 libgfortran5_10-20200324-1+rpi1 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200324-1+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7 libhogweed5_3.5.1+really3.5.1-2 libhwloc-dev_2.2.0+dfsg-3 libhwloc-plugins_2.2.0+dfsg-3 libhwloc15_2.2.0+dfsg-3 libibverbs-dev_28.0-1+b1 libibverbs1_28.0-1+b1 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-7 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7 libkrb5support0_1.17-7 libksba8_1.3.5-2 liblapack-dev_3.9.0-2 liblapack3_3.9.0-2 libldap-2.4-2_2.4.49+dfsg-2 libldap-common_2.4.49+dfsg-3 liblocale-gettext-perl_1.07-4 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libmpich-dev_3.4~a2+really3.3.2-1 libmpich12_3.4~a2+really3.3.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.0.2-5+rpi1 libopenmpi3_4.0.2-5+rpi1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpmix2_3.1.5-1 libprocps8_2:3.3.16-4 libpsl5_0.21.0-1 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.2-1 libpython3.8-stdlib_3.8.2-1 libreadline8_8.0-4 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-4 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1f-1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200324-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.3-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200324-1+rpi1 libuchardet0_0.0.6-3 libudev1_244.3-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.34.2-1 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libx11-dev_2:1.6.9-2 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxcb1-dev_1.14-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-4 libxnvctrl0_440.64-1 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 mpich_3.4~a2+really3.3.2-1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 ocl-icd-libopencl1_2.2.12-3 openmpi-bin_4.0.2-5+rpi1 openmpi-common_4.0.2-5+rpi1 openssh-client_1:8.2p1-4 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 procps_2:3.3.16-4 python3_3.8.2-3 python3-minimal_3.8.2-3 python3.8_3.8.2-1 python3.8-minimal_3.8.2-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2019c-3 util-linux_2.34-0.1 x11proto-core-dev_2019.2-1 x11proto-dev_2019.2-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Mar 8 04:13:07 2020 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2020.1-1.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2020.1.orig.tar.gz
dpkg-source: info: unpacking gromacs_2020.1-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying arm64-disable-numa-test.patch
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-576d08da-9072-4961-b4fb-a573fabb96a6
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2020.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON)
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/posts/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:216 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/posts/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.mpich"
-- Using manually set library suffix: "_mpi.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:216 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.mpich"
-- Using manually set library suffix: "_mpi_d.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich-dp
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.openmpi"
-- Using manually set library suffix: "_mpi.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.1-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:216 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.openmpi"
-- Using manually set library suffix: "_mpi_d.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.1-Raspbian-2020.1-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=/<<PKGBUILDDIR>>/src:/<<PKGBUILDDIR>>/python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.1-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target scanner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
[ 0%] Built target release-version-info
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target thread_mpi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target scanner
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 3%] Built target thread_mpi
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
Scanning dependencies of target vmddlopen
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 3%] Built target vmddlopen
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target view_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 9%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 10%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' {aka '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'int gmx_do_dssp(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1293:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1293 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1294 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1295 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1296 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs.so.5 -o ../../lib/libgromacs.so.5.0.0 CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/awh/awh.cpp.o CMakeFiles/libgromacs.dir/awh/bias.cpp.o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/awh/grid.cpp.o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o CMakeFiles/libgromacs.dir/tools/check.cpp.o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o CMakeFiles/libgromacs.dir/tools/dump.cpp.o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energyelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o fileio/CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.5.0.0 ../../lib/libgromacs.so.5 ../../lib/libgromacs.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target libgromacs
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/share/template /<<PKGBUILDDIR>>/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp /<<PKGBUILDDIR>>/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
Scanning dependencies of target template
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++14 -o CMakeFiles/template.dir/template.cpp.o -c /<<PKGBUILDDIR>>/share/template/template.cpp
Scanning dependencies of target gmxapi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target template
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target gmxapi
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -j4 -C build/basic-dp
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.1-Raspbian-2020.1-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=/<<PKGBUILDDIR>>/src:/<<PKGBUILDDIR>>/python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.1-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target scanner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
Scanning dependencies of target thread_mpi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
[ 0%] Built target release-version-info
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target scanner
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
Scanning dependencies of target vmddlopen
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target vmddlopen
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target view_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:67:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
67 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:85:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
85 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
366 | put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 7%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/9/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In function 'virtual void gmx::StatePropagatorData::trajectoryWriterTeardown(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 10%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' {aka '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1027:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1027 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1151:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1151 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1152 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:90:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
90 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' {aka '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:99:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
99 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:163:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
163 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<edpar> {anonymous}::read_edi_file(const char*, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' {aka '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_do_dssp(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In constructor 't_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'int gmx_nmtraj(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:55:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
55 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
64 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
101 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
70 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
90 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite2_param(InteractionsOfType*, int, int, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
77 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
84 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void convertInteractionsOfType(int, gmx::ArrayRef<const InteractionsOfType>, gmx::ArrayRef<const MoleculeInformation>, const MoleculeInformation*, int, double, real, gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<InteractionOfType, int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
252 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
847 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:888:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
888 | dih = clean_dih(dih, improper, atoms, rtpFFDB[0].bKeepAllGeneratedDihedrals,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
889 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:888:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:888:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
389 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2247 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' {aka '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/string:41,
from /usr/include/c++/9/stdexcept:39,
from /usr/include/c++/9/array:39,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' {aka '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/string:41,
from /usr/include/c++/9/stdexcept:39,
from /usr/include/c++/9/array:39,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/ext/new_allocator.h: In member function 'void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)':
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor 'InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:111:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
111 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function 'int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
342 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)':
/usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1305:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1305 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In function 'void sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual int gmx::{anonymous}::pdb2gmx::run()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2149:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2149 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
782 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
796 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
797 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
798 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
803 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
729 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:553:53: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
553 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
554 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:584:52: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
584 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
585 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function 'PreprocessingAtomTypes read_atype(const char*, t_symtab*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SpecialBond>::iterator' {aka '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<SpecialBond> generateSpecialBonds()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function 'void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
231 | InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function 'char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
135 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2658 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
541 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function 'void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
194 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2443 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2574 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
127 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
151 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
184 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1984 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function 'void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
340 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2336 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
711 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
730 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void add_param_to_list(InteractionsOfType*, const InteractionOfType&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
851 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1019 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1286 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void convert_moltype_couple(MoleculeInformation*, int, real, int, int, bool, int, InteractionsOfType*, warninp*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2606 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite4fdn_param(InteractionOfType*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:696:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
696 | static bool calc_vsite4fdn_param(InteractionOfType* vsite,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:696:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite4fd_param(InteractionOfType*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:639:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
639 | static bool calc_vsite4fd_param(InteractionOfType* vsite,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:639:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VsiteBondedInteraction>::iterator' {aka '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'int gmx_x2top(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
137 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:837:57: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
837 | bERROR = calc_vsite4fd_param(¶m, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
838 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:837:57: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:837:57: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:841:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
841 | bERROR = calc_vsite4fdn_param(¶m, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
842 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:841:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:841:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:583:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
583 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
714 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
715 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1245 | put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box, positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/9/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:356:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
356 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:165:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
165 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
166 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:948:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
948 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:948:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1000:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1000 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1000:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1150:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1150 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1150:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1380:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1380 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1380:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1389:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1389 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1389:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:437:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
437 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:451:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
451 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
452 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
453 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:509:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
509 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:519:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
519 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:533:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
533 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:257:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
257 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:762:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
762 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:766:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
766 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
767 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
768 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:780:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
780 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:823:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
823 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:828:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
828 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:931:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
931 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
932 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
933 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
934 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
935 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
936 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:958:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
958 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
959 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
960 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
961 | fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
962 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1113:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1113 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1141:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1141 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1149:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1149 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1165:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1165 | stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1172:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1172 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1173 | observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1174 | checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1175 | mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1207:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1207 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1279:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1279 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1280 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1286:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1293:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1293 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1294 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1295 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1296 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1303:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1303 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1406:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1406 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1442:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1442 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1463:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1463 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:845:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
845 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
846 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
847 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
848 | graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:905:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
905 | sum_dhdl(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, PaddedHostVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:385:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
385 | initialize_lambdas(fplog, *ir, MASTER(cr), &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1858:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1858 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1859 | static_cast<real>(step), &ems.s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1860 | observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2766:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2766 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2767 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2768 | fcd, state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2769 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2770 | state_work.s.lambda, &state_work.s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2771 | state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2772 | wcycle, graph, shellfc, fr, runScheduleWork, t, mu_tot,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2773 | vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
302 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:551:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
551 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:567:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
567 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:581:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
581 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
582 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:641:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
641 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, const gmx_vsite_t*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:936:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
936 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1094:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1094 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1095 | nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1096 | lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1097 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1188:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1188 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1189 | wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1191 | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/unique_ptr.h: In member function 'int gmx::Mdrunner::mdrunner()':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1384:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1384 | constructVsitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::LegacySimulator::do_tpi()':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:591:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:663:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
663 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
664 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
722 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:745:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
745 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
746 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
747 | &state_global->hist, f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
748 | state_global->lambda, nullptr, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
749 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
750 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:132:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
132 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:147:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
147 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:164:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
164 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:180:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
180 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:204:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
204 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
229 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 'void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:808:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
808 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs_d.so.5 -o ../../lib/libgromacs_d.so.5.0.0 CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/awh/awh.cpp.o CMakeFiles/libgromacs.dir/awh/bias.cpp.o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/awh/grid.cpp.o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o CMakeFiles/libgromacs.dir/tools/check.cpp.o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o CMakeFiles/libgromacs.dir/tools/dump.cpp.o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energyelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o fileio/CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.5.0.0 ../../lib/libgromacs_d.so.5 ../../lib/libgromacs_d.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target libgromacs
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/share/template /<<PKGBUILDDIR>>/build/basic-dp/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
Scanning dependencies of target template
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/share/template && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++14 -o CMakeFiles/template.dir/template.cpp.o -c /<<PKGBUILDDIR>>/share/template/template.cpp
Scanning dependencies of target gmxapi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target template
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target gmxapi
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -j4 -C build/basic tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 tests
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 96
/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.1-Raspbian-2020.1-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=/<<PKGBUILDDIR>>/src:/<<PKGBUILDDIR>>/python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.1-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target scanner
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 1%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 1%] Built target release-version-info
[ 3%] Built target thread_mpi
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
[ 3%] Built target lmfit_objlib
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
[ 4%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
[ 4%] Built target vmddlopen
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 5%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
Scanning dependencies of target gtest
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
[ 5%] Built target mdrun_objlib
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 65%] Built target libgromacs
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp /<<PKGBUILDDIR>>/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 66%] Built target gmxapi
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 66%] Built target gtest
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
Scanning dependencies of target gmock
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 66%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils /<<PKGBUILDDIR>>/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o
/usr/bin/ranlib ../../lib/libtestutils.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 68%] Built target testutils
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils/tests /<<PKGBUILDDIR>>/build/basic/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils/tests /<<PKGBUILDDIR>>/build/basic/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build
Scanning dependencies of target utility-mpi-test
Scanning dependencies of target testutils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target mdrun_test_infrastructure
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 68%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
[ 69%] Built target utility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
Scanning dependencies of target mdlib-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target mdrun_test_infrastructure
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
310 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::{anonymous}::iListInput; _Alloc = std::allocator<gmx::{anonymous}::iListInput>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:590:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
590 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:605:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
605 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:629:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
629 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:639:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
639 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:647:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
647 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' {aka '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target domdec-test
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 72%] Built target ewald-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target hardware-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target mdrunutility-test-shared
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target gpu_utils-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 77%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 77%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 77%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target options-test
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target random-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
[ 82%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target simd-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target gmxana-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
[ 85%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target pdb2gmx1-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target energyanalysis-test
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target mdrun-mpi-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-tpi-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target gmxapi-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target gmxapi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (14 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (3 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (5 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (34 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (4 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (45 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (3 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (3 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms)
1: [----------] 34 tests from ReferenceDataTest (102 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (3 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (2 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (10 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (153 ms total)
1: [ PASSED ] 59 tests.
1/52 Test #1: TestUtilsUnitTests .................. Passed 2.63 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (1 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (1 ms total)
2: [ PASSED ] 1 test.
2/52 Test #2: TestUtilsMpiUnitTests ............... Passed 0.10 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 346 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (1 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (1 ms)
3: [----------] 2 tests from CStringUtilityTest (1 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 3 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 3 tests from EnumerationHelpersTest (0 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (1 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (0 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (30 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (14 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (47 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (2 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
3: [----------] 6 tests from TreeValueTransformTest (6 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (1 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (2 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (1 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (4 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (9 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (1 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (1 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (18 ms)
3: [----------] 2 tests from PathTest (18 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (1 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (0 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (3 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (1 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (0 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms)
3: [----------] 10 tests from TextLineWrapperTest (5 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (1 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (1 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (0 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (1 ms)
3: [----------] 6 tests from TextWriterTest (3 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (1 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 346 tests from 56 test cases ran. (118 ms total)
3: [ PASSED ] 346 tests.
3/52 Test #3: UtilityUnitTests .................... Passed 0.24 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (3 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (8 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (11 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (12 ms total)
4: [ PASSED ] 2 tests.
4/52 Test #4: UtilityMpiUnitTests ................. Passed 0.11 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 149 tests from 11 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (3 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (33 ms)
5: [----------] 2 tests from PrEbinTest (38 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (1 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (2 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (3 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (1 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (0 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (5 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (14 ms)
5: [----------] 1 test from UpdateGroupsCog (16 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (1 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (53 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (24 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (3 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (50 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (21 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (12 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (13 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (208 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (35 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (12 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (145 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (8 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (8 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (8 ms)
5: [----------] 13 tests from WithParameters/SettleTest (58 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 149 tests from 11 test cases ran. (534 ms total)
5: [ PASSED ] 149 tests.
5/52 Test #5: MdlibUnitTest ....................... Passed 0.63 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (3 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (49 ms)
6: [----------] 2 tests from DensityFittingTest (52 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (5 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (1 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (0 ms)
6: [----------] 3 tests from ElectricFieldTest (1 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (59 ms total)
6: [ PASSED ] 20 tests.
6/52 Test #6: AppliedForcesUnitTest ............... Passed 0.12 sec
test 7
Start 7: ListedForcesTest
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ListedForcesTest.xml"
7: Test timeout computed to be: 30
7: [==========] Running 315 tests from 5 test cases.
7: [----------] Global test environment set-up.
7: [----------] 72 tests from Bond/ListedForcesTest
7: [ RUN ] Bond/ListedForcesTest.Ifunc/0
7: [ OK ] Bond/ListedForcesTest.Ifunc/0 (23 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/1
7: [ OK ] Bond/ListedForcesTest.Ifunc/1 (6 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/2
7: [ OK ] Bond/ListedForcesTest.Ifunc/2 (5 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/3
7: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/4
7: [ OK ] Bond/ListedForcesTest.Ifunc/4 (7 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/5
7: [ OK ] Bond/ListedForcesTest.Ifunc/5 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/6
7: [ OK ] Bond/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/7
7: [ OK ] Bond/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/8
7: [ OK ] Bond/ListedForcesTest.Ifunc/8 (12 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/9
7: [ OK ] Bond/ListedForcesTest.Ifunc/9 (10 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/10
7: [ OK ] Bond/ListedForcesTest.Ifunc/10 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/11
7: [ OK ] Bond/ListedForcesTest.Ifunc/11 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/12
7: [ OK ] Bond/ListedForcesTest.Ifunc/12 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/13
7: [ OK ] Bond/ListedForcesTest.Ifunc/13 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/14
7: [ OK ] Bond/ListedForcesTest.Ifunc/14 (18 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/15
7: [ OK ] Bond/ListedForcesTest.Ifunc/15 (14 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/16
7: [ OK ] Bond/ListedForcesTest.Ifunc/16 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/17
7: [ OK ] Bond/ListedForcesTest.Ifunc/17 (6 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/18
7: [ OK ] Bond/ListedForcesTest.Ifunc/18 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/19
7: [ OK ] Bond/ListedForcesTest.Ifunc/19 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/20
7: [ OK ] Bond/ListedForcesTest.Ifunc/20 (13 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/21
7: [ OK ] Bond/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/22
7: [ OK ] Bond/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/23
7: [ OK ] Bond/ListedForcesTest.Ifunc/23 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/24
7: [ OK ] Bond/ListedForcesTest.Ifunc/24 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/25
7: [ OK ] Bond/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/26
7: [ OK ] Bond/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/27
7: [ OK ] Bond/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/28
7: [ OK ] Bond/ListedForcesTest.Ifunc/28 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/29
7: [ OK ] Bond/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/30
7: [ OK ] Bond/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/31
7: [ OK ] Bond/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/32
7: [ OK ] Bond/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/33
7: [ OK ] Bond/ListedForcesTest.Ifunc/33 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/34
7: [ OK ] Bond/ListedForcesTest.Ifunc/34 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/35
7: [ OK ] Bond/ListedForcesTest.Ifunc/35 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/36
7: [ OK ] Bond/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/37
7: [ OK ] Bond/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/38
7: [ OK ] Bond/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/39
7: [ OK ] Bond/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/40
7: [ OK ] Bond/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/41
7: [ OK ] Bond/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/42
7: [ OK ] Bond/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/43
7: [ OK ] Bond/ListedForcesTest.Ifunc/43 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/44
7: [ OK ] Bond/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/45
7: [ OK ] Bond/ListedForcesTest.Ifunc/45 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/46
7: [ OK ] Bond/ListedForcesTest.Ifunc/46 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/47
7: [ OK ] Bond/ListedForcesTest.Ifunc/47 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/48
7: [ OK ] Bond/ListedForcesTest.Ifunc/48 (18 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/49
7: [ OK ] Bond/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/50
7: [ OK ] Bond/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/51
7: [ OK ] Bond/ListedForcesTest.Ifunc/51 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/52
7: [ OK ] Bond/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/53
7: [ OK ] Bond/ListedForcesTest.Ifunc/53 (12 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/54
7: [ OK ] Bond/ListedForcesTest.Ifunc/54 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/55
7: [ OK ] Bond/ListedForcesTest.Ifunc/55 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/56
7: [ OK ] Bond/ListedForcesTest.Ifunc/56 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/57
7: [ OK ] Bond/ListedForcesTest.Ifunc/57 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/58
7: [ OK ] Bond/ListedForcesTest.Ifunc/58 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/59
7: [ OK ] Bond/ListedForcesTest.Ifunc/59 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/60
7: [ OK ] Bond/ListedForcesTest.Ifunc/60 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/61
7: [ OK ] Bond/ListedForcesTest.Ifunc/61 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/62
7: [ OK ] Bond/ListedForcesTest.Ifunc/62 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/63
7: [ OK ] Bond/ListedForcesTest.Ifunc/63 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/64
7: [ OK ] Bond/ListedForcesTest.Ifunc/64 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/65
7: [ OK ] Bond/ListedForcesTest.Ifunc/65 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/66
7: [ OK ] Bond/ListedForcesTest.Ifunc/66 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/67
7: [ OK ] Bond/ListedForcesTest.Ifunc/67 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/68
7: [ OK ] Bond/ListedForcesTest.Ifunc/68 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/69
7: [ OK ] Bond/ListedForcesTest.Ifunc/69 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/70
7: [ OK ] Bond/ListedForcesTest.Ifunc/70 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/71
7: [ OK ] Bond/ListedForcesTest.Ifunc/71 (2 ms)
7: [----------] 72 tests from Bond/ListedForcesTest (277 ms total)
7:
7: [----------] 99 tests from Angle/ListedForcesTest
7: [ RUN ] Angle/ListedForcesTest.Ifunc/0
7: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/1
7: [ OK ] Angle/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/2
7: [ OK ] Angle/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/3
7: [ OK ] Angle/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/4
7: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/5
7: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/6
7: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/7
7: [ OK ] Angle/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/8
7: [ OK ] Angle/ListedForcesTest.Ifunc/8 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/9
7: [ OK ] Angle/ListedForcesTest.Ifunc/9 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/10
7: [ OK ] Angle/ListedForcesTest.Ifunc/10 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/11
7: [ OK ] Angle/ListedForcesTest.Ifunc/11 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/12
7: [ OK ] Angle/ListedForcesTest.Ifunc/12 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/13
7: [ OK ] Angle/ListedForcesTest.Ifunc/13 (3 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/14
7: [ OK ] Angle/ListedForcesTest.Ifunc/14 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/15
7: [ OK ] Angle/ListedForcesTest.Ifunc/15 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/16
7: [ OK ] Angle/ListedForcesTest.Ifunc/16 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/17
7: [ OK ] Angle/ListedForcesTest.Ifunc/17 (3 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/18
7: [ OK ] Angle/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/19
7: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/20
7: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/21
7: [ OK ] Angle/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/22
7: [ OK ] Angle/ListedForcesTest.Ifunc/22 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/23
7: [ OK ] Angle/ListedForcesTest.Ifunc/23 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/24
7: [ OK ] Angle/ListedForcesTest.Ifunc/24 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/25
7: [ OK ] Angle/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/26
7: [ OK ] Angle/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/27
7: [ OK ] Angle/ListedForcesTest.Ifunc/27 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/28
7: [ OK ] Angle/ListedForcesTest.Ifunc/28 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/29
7: [ OK ] Angle/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/30
7: [ OK ] Angle/ListedForcesTest.Ifunc/30 (3 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/31
7: [ OK ] Angle/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/32
7: [ OK ] Angle/ListedForcesTest.Ifunc/32 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/33
7: [ OK ] Angle/ListedForcesTest.Ifunc/33 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/34
7: [ OK ] Angle/ListedForcesTest.Ifunc/34 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/35
7: [ OK ] Angle/ListedForcesTest.Ifunc/35 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/36
7: [ OK ] Angle/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/37
7: [ OK ] Angle/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/38
7: [ OK ] Angle/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/39
7: [ OK ] Angle/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/40
7: [ OK ] Angle/ListedForcesTest.Ifunc/40 (27 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/41
7: [ OK ] Angle/ListedForcesTest.Ifunc/41 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/42
7: [ OK ] Angle/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/43
7: [ OK ] Angle/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/44
7: [ OK ] Angle/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/45
7: [ OK ] Angle/ListedForcesTest.Ifunc/45 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/46
7: [ OK ] Angle/ListedForcesTest.Ifunc/46 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/47
7: [ OK ] Angle/ListedForcesTest.Ifunc/47 (3 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/48
7: [ OK ] Angle/ListedForcesTest.Ifunc/48 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/49
7: [ OK ] Angle/ListedForcesTest.Ifunc/49 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/50
7: [ OK ] Angle/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/51
7: [ OK ] Angle/ListedForcesTest.Ifunc/51 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/52
7: [ OK ] Angle/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/53
7: [ OK ] Angle/ListedForcesTest.Ifunc/53 (3 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/54
7: [ OK ] Angle/ListedForcesTest.Ifunc/54 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/55
7: [ OK ] Angle/ListedForcesTest.Ifunc/55 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/56
7: [ OK ] Angle/ListedForcesTest.Ifunc/56 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/57
7: [ OK ] Angle/ListedForcesTest.Ifunc/57 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/58
7: [ OK ] Angle/ListedForcesTest.Ifunc/58 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/59
7: [ OK ] Angle/ListedForcesTest.Ifunc/59 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/60
7: [ OK ] Angle/ListedForcesTest.Ifunc/60 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/61
7: [ OK ] Angle/ListedForcesTest.Ifunc/61 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/62
7: [ OK ] Angle/ListedForcesTest.Ifunc/62 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/63
7: [ OK ] Angle/ListedForcesTest.Ifunc/63 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/64
7: [ OK ] Angle/ListedForcesTest.Ifunc/64 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/65
7: [ OK ] Angle/ListedForcesTest.Ifunc/65 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/66
7: [ OK ] Angle/ListedForcesTest.Ifunc/66 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/67
7: [ OK ] Angle/ListedForcesTest.Ifunc/67 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/68
7: [ OK ] Angle/ListedForcesTest.Ifunc/68 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/69
7: [ OK ] Angle/ListedForcesTest.Ifunc/69 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/70
7: [ OK ] Angle/ListedForcesTest.Ifunc/70 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/71
7: [ OK ] Angle/ListedForcesTest.Ifunc/71 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/72
7: [ OK ] Angle/ListedForcesTest.Ifunc/72 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/73
7: [ OK ] Angle/ListedForcesTest.Ifunc/73 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/74
7: [ OK ] Angle/ListedForcesTest.Ifunc/74 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/75
7: [ OK ] Angle/ListedForcesTest.Ifunc/75 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/76
7: [ OK ] Angle/ListedForcesTest.Ifunc/76 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/77
7: [ OK ] Angle/ListedForcesTest.Ifunc/77 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/78
7: [ OK ] Angle/ListedForcesTest.Ifunc/78 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/79
7: [ OK ] Angle/ListedForcesTest.Ifunc/79 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/80
7: [ OK ] Angle/ListedForcesTest.Ifunc/80 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/81
7: [ OK ] Angle/ListedForcesTest.Ifunc/81 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/82
7: [ OK ] Angle/ListedForcesTest.Ifunc/82 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/83
7: [ OK ] Angle/ListedForcesTest.Ifunc/83 (12 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/84
7: [ OK ] Angle/ListedForcesTest.Ifunc/84 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/85
7: [ OK ] Angle/ListedForcesTest.Ifunc/85 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/86
7: [ OK ] Angle/ListedForcesTest.Ifunc/86 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/87
7: [ OK ] Angle/ListedForcesTest.Ifunc/87 (3 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/88
7: [ OK ] Angle/ListedForcesTest.Ifunc/88 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/89
7: [ OK ] Angle/ListedForcesTest.Ifunc/89 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/90
7: [ OK ] Angle/ListedForcesTest.Ifunc/90 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/91
7: [ OK ] Angle/ListedForcesTest.Ifunc/91 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/92
7: [ OK ] Angle/ListedForcesTest.Ifunc/92 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/93
7: [ OK ] Angle/ListedForcesTest.Ifunc/93 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/94
7: [ OK ] Angle/ListedForcesTest.Ifunc/94 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/95
7: [ OK ] Angle/ListedForcesTest.Ifunc/95 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/96
7: [ OK ] Angle/ListedForcesTest.Ifunc/96 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/97
7: [ OK ] Angle/ListedForcesTest.Ifunc/97 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/98
7: [ OK ] Angle/ListedForcesTest.Ifunc/98 (1 ms)
7: [----------] 99 tests from Angle/ListedForcesTest (215 ms total)
7:
7: [----------] 54 tests from Dihedral/ListedForcesTest
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/18
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/19
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/20
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/21
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/21 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/22
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/23
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/24
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/25
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/26
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/27
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/27 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/28
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/28 (4 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/29
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/29 (3 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/30
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/30 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/31
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/32
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/32 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/33
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/33 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/34
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/34 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/35
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/35 (3 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/36
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/36 (24 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/37
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/37 (4 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/38
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/38 (3 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/39
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/39 (3 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/40
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/40 (3 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/41
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/41 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/42
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/42 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/43
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/44
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/44 (3 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/45
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/46
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/47
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/47 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/48
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/49
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/50
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/51
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/51 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/52
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/52 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/53
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/53 (1 ms)
7: [----------] 54 tests from Dihedral/ListedForcesTest (122 ms total)
7:
7: [----------] 36 tests from Polarize/ListedForcesTest
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
7: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
7: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
7: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
7: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
7: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
7: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
7: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
7: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
7: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
7: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
7: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
7: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/12
7: [ OK ] Polarize/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/13
7: [ OK ] Polarize/ListedForcesTest.Ifunc/13 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/14
7: [ OK ] Polarize/ListedForcesTest.Ifunc/14 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/15
7: [ OK ] Polarize/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/16
7: [ OK ] Polarize/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/17
7: [ OK ] Polarize/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/18
7: [ OK ] Polarize/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/19
7: [ OK ] Polarize/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/20
7: [ OK ] Polarize/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/21
7: [ OK ] Polarize/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/22
7: [ OK ] Polarize/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/23
7: [ OK ] Polarize/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/24
7: [ OK ] Polarize/ListedForcesTest.Ifunc/24 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/25
7: [ OK ] Polarize/ListedForcesTest.Ifunc/25 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/26
7: [ OK ] Polarize/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/27
7: [ OK ] Polarize/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/28
7: [ OK ] Polarize/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/29
7: [ OK ] Polarize/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/30
7: [ OK ] Polarize/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/31
7: [ OK ] Polarize/ListedForcesTest.Ifunc/31 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/32
7: [ OK ] Polarize/ListedForcesTest.Ifunc/32 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/33
7: [ OK ] Polarize/ListedForcesTest.Ifunc/33 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/34
7: [ OK ] Polarize/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/35
7: [ OK ] Polarize/ListedForcesTest.Ifunc/35 (1 ms)
7: [----------] 36 tests from Polarize/ListedForcesTest (34 ms total)
7:
7: [----------] 54 tests from Restraints/ListedForcesTest
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
7: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
7: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (3 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
7: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
7: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
7: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
7: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
7: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
7: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
7: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
7: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
7: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
7: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
7: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
7: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
7: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
7: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
7: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
7: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/18
7: [ OK ] Restraints/ListedForcesTest.Ifunc/18 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/19
7: [ OK ] Restraints/ListedForcesTest.Ifunc/19 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/20
7: [ OK ] Restraints/ListedForcesTest.Ifunc/20 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/21
7: [ OK ] Restraints/ListedForcesTest.Ifunc/21 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/22
7: [ OK ] Restraints/ListedForcesTest.Ifunc/22 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/23
7: [ OK ] Restraints/ListedForcesTest.Ifunc/23 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/24
7: [ OK ] Restraints/ListedForcesTest.Ifunc/24 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/25
7: [ OK ] Restraints/ListedForcesTest.Ifunc/25 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/26
7: [ OK ] Restraints/ListedForcesTest.Ifunc/26 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/27
7: [ OK ] Restraints/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/28
7: [ OK ] Restraints/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/29
7: [ OK ] Restraints/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/30
7: [ OK ] Restraints/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/31
7: [ OK ] Restraints/ListedForcesTest.Ifunc/31 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/32
7: [ OK ] Restraints/ListedForcesTest.Ifunc/32 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/33
7: [ OK ] Restraints/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/34
7: [ OK ] Restraints/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/35
7: [ OK ] Restraints/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/36
7: [ OK ] Restraints/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/37
7: [ OK ] Restraints/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/38
7: [ OK ] Restraints/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/39
7: [ OK ] Restraints/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/40
7: [ OK ] Restraints/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/41
7: [ OK ] Restraints/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/42
7: [ OK ] Restraints/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/43
7: [ OK ] Restraints/ListedForcesTest.Ifunc/43 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/44
7: [ OK ] Restraints/ListedForcesTest.Ifunc/44 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/45
7: [ OK ] Restraints/ListedForcesTest.Ifunc/45 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/46
7: [ OK ] Restraints/ListedForcesTest.Ifunc/46 (10 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/47
7: [ OK ] Restraints/ListedForcesTest.Ifunc/47 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/48
7: [ OK ] Restraints/ListedForcesTest.Ifunc/48 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/49
7: [ OK ] Restraints/ListedForcesTest.Ifunc/49 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/50
7: [ OK ] Restraints/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/51
7: [ OK ] Restraints/ListedForcesTest.Ifunc/51 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/52
7: [ OK ] Restraints/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/53
7: [ OK ] Restraints/ListedForcesTest.Ifunc/53 (2 ms)
7: [----------] 54 tests from Restraints/ListedForcesTest (89 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 315 tests from 5 test cases ran. (740 ms total)
7: [ PASSED ] 315 tests.
7/52 Test #7: ListedForcesTest .................... Passed 0.94 sec
test 8
Start 8: CommandLineUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 7 test cases.
8: [----------] Global test environment set-up.
8: [----------] 3 tests from CommandLineHelpModuleTest
8: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
8: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (17 ms)
8: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
8: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
8: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
8: [ OK ] CommandLineHelpModuleTest.ExportsHelp (20 ms)
8: [----------] 3 tests from CommandLineHelpModuleTest (39 ms total)
8:
8: [----------] 7 tests from CommandLineHelpWriterTest
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
8: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (14 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
8: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
8: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
8: [----------] 7 tests from CommandLineHelpWriterTest (24 ms total)
8:
8: [----------] 6 tests from CommandLineModuleManagerTest
8: [ RUN ] CommandLineModuleManagerTest.RunsModule
8: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
8: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
8: [----------] 6 tests from CommandLineModuleManagerTest (6 ms total)
8:
8: [----------] 13 tests from CommandLineParserTest
8: [ RUN ] CommandLineParserTest.HandlesSingleValues
8: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
8: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
8: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesString
8: [ OK ] CommandLineParserTest.HandlesString (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
8: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
8: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
8: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
8: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
8: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
8: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
8: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
8: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
8: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (1 ms)
8: [----------] 13 tests from CommandLineParserTest (6 ms total)
8:
8: [----------] 6 tests from CommandLineProgramContextTest
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (1 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms)
8: [----------] 6 tests from CommandLineProgramContextTest (3 ms total)
8:
8: [----------] 3 tests from OutputNamesTest
8: [ RUN ] OutputNamesTest.CanBeSuffixed
8: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
8: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
8: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
8: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
8: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
8: [----------] 3 tests from OutputNamesTest (1 ms total)
8:
8: [----------] 21 tests from ParseCommonArgsTest
8: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
8: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
8: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
8: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
8: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
8: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
8: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (1 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
8: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
8: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
8: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
8: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
8: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
8: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (3 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
8: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
8: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (1 ms)
8: [----------] 21 tests from ParseCommonArgsTest (20 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 7 test cases ran. (101 ms total)
8: [ PASSED ] 59 tests.
8/52 Test #8: CommandLineUnitTests ................ Passed 0.17 sec
test 9
Start 9: DomDecTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 9 tests from 2 test cases.
9: [----------] Global test environment set-up.
9: [----------] 7 tests from HashedMap
9: [ RUN ] HashedMap.InsertsFinds
9: [ OK ] HashedMap.InsertsFinds (0 ms)
9: [ RUN ] HashedMap.NegativeKeysWork
9: [ OK ] HashedMap.NegativeKeysWork (0 ms)
9: [ RUN ] HashedMap.InsertsErases
9: [ OK ] HashedMap.InsertsErases (0 ms)
9: [ RUN ] HashedMap.InsertsOrAssigns
9: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
9: [ RUN ] HashedMap.Clears
9: [ OK ] HashedMap.Clears (0 ms)
9: [ RUN ] HashedMap.LinkedEntries
9: [ OK ] HashedMap.LinkedEntries (0 ms)
9: [ RUN ] HashedMap.ResizesTable
9: [ OK ] HashedMap.ResizesTable (0 ms)
9: [----------] 7 tests from HashedMap (0 ms total)
9:
9: [----------] 2 tests from LocalAtomSetManager
9: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
9: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
9: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
9: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
9: [----------] 2 tests from LocalAtomSetManager (0 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 9 tests from 2 test cases ran. (1 ms total)
9: [ PASSED ] 9 tests.
9/52 Test #9: DomDecTests ......................... Passed 0.06 sec
test 10
Start 10: EwaldUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 257 tests from 10 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (13 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms)
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (15 ms total)
10:
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (43 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (10 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (9 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (19 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (23 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (10 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (25 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (10 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (10 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (10 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (34 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (12 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (12 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (12 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (12 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (12 ms)
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (373 ms total)
10:
10: [----------] 144 tests from SaneInput/PmeGatherTest
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (4 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (10 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (4 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
10: [----------] 144 tests from SaneInput/PmeGatherTest (313 ms total)
10:
10: [----------] 16 tests from SaneInput/PmeSolveTest
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (7 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (8 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (8 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (10 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (5 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (9 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (5 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (10 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (3 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (5 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (3 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (6 ms)
10: [----------] 16 tests from SaneInput/PmeSolveTest (104 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (4 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (34 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (5 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (5 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (60 ms total)
10:
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (3 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (6 ms)
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (95 ms total)
10:
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (15 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (9 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (10 ms)
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (102 ms total)
10:
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (10 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (11 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (10 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (14 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (15 ms)
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (120 ms total)
10:
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (17 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (18 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (25 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (27 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (37 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (39 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (17 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (18 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (24 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (27 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (33 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (39 ms)
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (346 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 257 tests from 10 test cases ran. (2118 ms total)
10: [ PASSED ] 257 tests.
10/52 Test #10: EwaldUnitTests ...................... Passed 2.33 sec
test 11
Start 11: FFTUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 14 tests from 4 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ManyFFTTest
11: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (39 ms)
11: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (51 ms)
11: [----------] 2 tests from ManyFFTTest (94 ms total)
11:
11: [----------] 1 test from FFTTest
11: [ RUN ] FFTTest.Real2DLength18_15Test
11: [ OK ] FFTTest.Real2DLength18_15Test (20 ms)
11: [----------] 1 test from FFTTest (21 ms total)
11:
11: [----------] 1 test from FFFTest3D
11: [ RUN ] FFFTest3D.Real5_6_9
11: [ OK ] FFFTest3D.Real5_6_9 (12 ms)
11: [----------] 1 test from FFFTest3D (13 ms total)
11:
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (4 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (15 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (12 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (9 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (31 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (43 ms)
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (129 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 14 tests from 4 test cases ran. (258 ms total)
11: [ PASSED ] 14 tests.
11/52 Test #11: FFTUnitTests ........................ Passed 0.32 sec
test 12
Start 12: GpuUtilsUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 62 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 2 tests from ClfftInitializer
12: [ RUN ] ClfftInitializer.SingleInitializationWorks
12: [ OK ] ClfftInitializer.SingleInitializationWorks (1 ms)
12: [ RUN ] ClfftInitializer.TwoInitializationsWork
12: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
12: [----------] 2 tests from ClfftInitializer (1 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
12: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/0 (1 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
12: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/1 (1 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/3 (1 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/0 (2 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
12: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/1 (1 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
12: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Swap
12: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Comparison
12: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
12: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
12: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Swap
12: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Comparison
12: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
12: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Swap
12: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Comparison
12: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
12: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Swap
12: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Comparison
12: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
12:
12: [----------] 1 test from HostAllocatorUntypedTest
12: [ RUN ] HostAllocatorUntypedTest.Comparison
12: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
12: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
12:
12: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.Move
12: [ OK ] AllocatorTest/0.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/0 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.Move
12: [ OK ] AllocatorTest/1.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/1 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.Move
12: [ OK ] AllocatorTest/2.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/2 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.Move
12: [ OK ] AllocatorTest/3.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/3 (1 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 62 tests from 20 test cases ran. (18 ms total)
12: [ PASSED ] 62 tests.
12/52 Test #12: GpuUtilsUnitTests ................... Passed 0.09 sec
test 13
Start 13: HardwareUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 4 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 4 tests from HardwareTopologyTest
13: [ RUN ] HardwareTopologyTest.Execute
13: [ OK ] HardwareTopologyTest.Execute (34 ms)
13: [ RUN ] HardwareTopologyTest.HwlocExecute
13: [ OK ] HardwareTopologyTest.HwlocExecute (32 ms)
13: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
13: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (33 ms)
13: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
13: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (31 ms)
13: [----------] 4 tests from HardwareTopologyTest (130 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 4 tests from 1 test case ran. (131 ms total)
13: [ PASSED ] 4 tests.
13/52 Test #13: HardwareUnitTests ................... Passed 0.19 sec
test 14
Start 14: MathUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 204 tests from 29 test cases.
14: [----------] Global test environment set-up.
14: [----------] 1 test from EmptyArrayRefWithPaddingTest
14: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
14:
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
14: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
14: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
14: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
14: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
14:
14: [----------] 8 tests from TranslateAndScaleTest
14: [ RUN ] TranslateAndScaleTest.identityTransformation
14: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms)
14: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
14: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
14: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (1 ms)
14: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
14: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingIdentity
14: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
14: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
14: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
14: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (1 ms)
14: [----------] 8 tests from TranslateAndScaleTest (2 ms total)
14:
14: [----------] 12 tests from DensitySimilarityTest
14: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
14: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
14: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
14: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (12 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (122 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (134 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (122 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (2 ms)
14: [----------] 12 tests from DensitySimilarityTest (394 ms total)
14:
14: [----------] 6 tests from StructureSimilarityTest
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
14: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
14: [----------] 6 tests from StructureSimilarityTest (0 ms total)
14:
14: [----------] 8 tests from ExponentialMovingAverage
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
14: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
14: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
14: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
14: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
14: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
14: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
14: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
14: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
14: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
14: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
14: [----------] 8 tests from ExponentialMovingAverage (1 ms total)
14:
14: [----------] 21 tests from FunctionTest
14: [ RUN ] FunctionTest.StaticLog2
14: [ OK ] FunctionTest.StaticLog2 (1 ms)
14: [ RUN ] FunctionTest.Log2I32Bit
14: [ OK ] FunctionTest.Log2I32Bit (1 ms)
14: [ RUN ] FunctionTest.Log2I64Bit
14: [ OK ] FunctionTest.Log2I64Bit (1 ms)
14: [ RUN ] FunctionTest.GreatestCommonDivisor
14: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
14: [ RUN ] FunctionTest.InvsqrtFloat
14: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
14: [ RUN ] FunctionTest.InvsqrtDouble
14: [ OK ] FunctionTest.InvsqrtDouble (1 ms)
14: [ RUN ] FunctionTest.InvsqrtInteger
14: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
14: [ RUN ] FunctionTest.InvcbrtFloat
14: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
14: [ RUN ] FunctionTest.InvcbrtDouble
14: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
14: [ RUN ] FunctionTest.InvcbrtInteger
14: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
14: [ RUN ] FunctionTest.SixthrootFloat
14: [ OK ] FunctionTest.SixthrootFloat (1 ms)
14: [ RUN ] FunctionTest.SixthrootDouble
14: [ OK ] FunctionTest.SixthrootDouble (1 ms)
14: [ RUN ] FunctionTest.SixthrootInteger
14: [ OK ] FunctionTest.SixthrootInteger (0 ms)
14: [ RUN ] FunctionTest.InvsixthrootFloat
14: [ OK ] FunctionTest.InvsixthrootFloat (1 ms)
14: [ RUN ] FunctionTest.InvsixthrootDouble
14: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
14: [ RUN ] FunctionTest.InvsixthrootInteger
14: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
14: [ RUN ] FunctionTest.Powers
14: [ OK ] FunctionTest.Powers (0 ms)
14: [ RUN ] FunctionTest.ErfInvFloat
14: [ OK ] FunctionTest.ErfInvFloat (1 ms)
14: [ RUN ] FunctionTest.ErfInvDouble
14: [ OK ] FunctionTest.ErfInvDouble (1 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (2 ms)
14: [----------] 21 tests from FunctionTest (16 ms total)
14:
14: [----------] 4 tests from GaussianOn1DLattice
14: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
14: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
14: [ RUN ] GaussianOn1DLattice.isCorrect
14: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
14: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
14: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
14: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
14: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
14: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
14:
14: [----------] 9 tests from GaussTransformTest
14: [ RUN ] GaussTransformTest.isZeroUponConstruction
14: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
14: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
14: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
14: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
14: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
14: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
14: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
14: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
14: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
14: [ RUN ] GaussTransformTest.view
14: [ OK ] GaussTransformTest.view (0 ms)
14: [----------] 9 tests from GaussTransformTest (1 ms total)
14:
14: [----------] 3 tests from DensityFittingForce
14: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
14: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
14: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
14: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
14: [ RUN ] DensityFittingForce.pullsTowardsDerivative
14: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
14: [----------] 3 tests from DensityFittingForce (0 ms total)
14:
14: [----------] 2 tests from InvertMatrixTest
14: [ RUN ] InvertMatrixTest.IdentityIsImpotent
14: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertMatrixTest.ComputesInverse
14: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
14: [----------] 2 tests from InvertMatrixTest (1 ms total)
14:
14: [----------] 2 tests from InvertBoxMatrixTest
14: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
14: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
14: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
14: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
14:
14: [----------] 15 tests from MatrixTest
14: [ RUN ] MatrixTest.canSetFromArray
14: [ OK ] MatrixTest.canSetFromArray (0 ms)
14: [ RUN ] MatrixTest.canSetStaticallyFromList
14: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
14: [ RUN ] MatrixTest.canConstructAndFill
14: [ OK ] MatrixTest.canConstructAndFill (0 ms)
14: [ RUN ] MatrixTest.canSetValues
14: [ OK ] MatrixTest.canSetValues (0 ms)
14: [ RUN ] MatrixTest.canCopyAssign
14: [ OK ] MatrixTest.canCopyAssign (0 ms)
14: [ RUN ] MatrixTest.canSwap
14: [ OK ] MatrixTest.canSwap (0 ms)
14: [ RUN ] MatrixTest.staticMultiDimArrayExtent
14: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MatrixTest.determinantWorks
14: [ OK ] MatrixTest.determinantWorks (0 ms)
14: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
14: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
14: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
14: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
14: [ RUN ] MatrixTest.traceWorks
14: [ OK ] MatrixTest.traceWorks (0 ms)
14: [ RUN ] MatrixTest.transposeWorks
14: [ OK ] MatrixTest.transposeWorks (0 ms)
14: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
14: [ OK ] MatrixTest.transposeOfSymmetricMatrix (1 ms)
14: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
14: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
14: [ RUN ] MatrixTest.canFillLegacyMatrix
14: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
14: [----------] 15 tests from MatrixTest (1 ms total)
14:
14: [----------] 25 tests from MultiDimArrayTest
14: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
14: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
14: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
14: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
14: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
14: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
14: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
14: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
14: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
14: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
14: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
14: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
14: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapStatic
14: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapDynamic
14: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToView
14: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToConstView
14: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
14: [ RUN ] MultiDimArrayTest.viewBegin
14: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.viewEnd
14: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstBegin
14: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstEnd
14: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
14: [----------] 25 tests from MultiDimArrayTest (1 ms total)
14:
14: [----------] 4 tests from MultiDimArrayToMdSpanTest
14: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
14: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
14: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanCopyAssign
14: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanMoveAssign
14: [ OK ] PaddedVectorTest/0.CanMoveAssign (1 ms)
14: [ RUN ] PaddedVectorTest/0.CanSwap
14: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/0 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
14: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanCopyAssign
14: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanMoveAssign
14: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanSwap
14: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
14: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanCopyAssign
14: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanMoveAssign
14: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanSwap
14: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
14: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanCopyAssign
14: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanMoveAssign
14: [ OK ] PaddedVectorTest/3.CanMoveAssign (1 ms)
14: [ RUN ] PaddedVectorTest/3.CanSwap
14: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/3 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
14: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanCopyAssign
14: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanMoveAssign
14: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanSwap
14: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanCopyAssign
14: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanMoveAssign
14: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanSwap
14: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanCopyAssign
14: [ OK ] PaddedVectorTest/6.CanCopyAssign (1 ms)
14: [ RUN ] PaddedVectorTest/6.CanMoveAssign
14: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanSwap
14: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/6 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanCopyAssign
14: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanMoveAssign
14: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanSwap
14: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanCopyAssign
14: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanMoveAssign
14: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanSwap
14: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanCopyAssign
14: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanMoveAssign
14: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanSwap
14: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
14:
14: [----------] 37 tests from RVecTest
14: [ RUN ] RVecTest.CanBeStoredInVector
14: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAsMutable_rvec
14: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Array
14: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
14: [ RUN ] RVecTest.CanAddRVecToRvec
14: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanAddAssignRVecToRvec
14: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractRVecFromRvec
14: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
14: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanDotProductRVecByRvec
14: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanCrossProductRVecByRvec
14: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVecInplace
14: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
14: [ RUN ] RVecTest.CanScaleRVec
14: [ OK ] RVecTest.CanScaleRVec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVec
14: [ OK ] RVecTest.CanDivideRVec (0 ms)
14: [ RUN ] RVecTest.CanDoUnitvFromRVec
14: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanSqLengthOfRVec
14: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanLengthOfRVec
14: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToRVec
14: [ OK ] RVecTest.CanCastToRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToDVec
14: [ OK ] RVecTest.CanCastToDVec (0 ms)
14: [ RUN ] RVecTest.CanLeftScalarMultiply
14: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanRightScalarMultiply
14: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanGetUnitvFromRVec
14: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanGetSqLengthOfRVec
14: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanGetLengthOfRVec
14: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoCrossProductOfRVec
14: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoDotProductOfRVec
14: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanScaleByVector
14: [ OK ] RVecTest.CanScaleByVector (0 ms)
14: [ RUN ] RVecTest.asIVec
14: [ OK ] RVecTest.asIVec (0 ms)
14: [ RUN ] RVecTest.elementWiseMin
14: [ OK ] RVecTest.elementWiseMin (0 ms)
14: [ RUN ] RVecTest.elementWiseMax
14: [ OK ] RVecTest.elementWiseMax (0 ms)
14: [ RUN ] RVecTest.WorksAs_dvec_Reference
14: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_ivec_Reference
14: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Reference
14: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
14: [ RUN ] RVecTest.CopyConstructorWorks
14: [ OK ] RVecTest.CopyConstructorWorks (1 ms)
14: [ RUN ] RVecTest.CopyAssignmentWorks
14: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
14: [ RUN ] RVecTest.MoveConstructorWorks
14: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
14: [ RUN ] RVecTest.MoveAssignmentWorks
14: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
14: [----------] 37 tests from RVecTest (2 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 204 tests from 29 test cases ran. (426 ms total)
14: [ PASSED ] 204 tests.
14/52 Test #14: MathUnitTests ....................... Passed 0.51 sec
test 15
Start 15: MdrunUtilityUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 17 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 17 tests from ThreadAffinityTest
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
15: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
15: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (2 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (2 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
15: NOTE: Affinity setting failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
15: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
15: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
15: NOTE: Affinity setting for 1/2 threads failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
15: [----------] 17 tests from ThreadAffinityTest (22 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 17 tests from 1 test case ran. (22 ms total)
15: [ PASSED ] 17 tests.
15/52 Test #15: MdrunUtilityUnitTests ............... Passed 0.09 sec
test 16
Start 16: MdrunUtilityMpiUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 13 tests from 2 test cases.
16: [----------] Global test environment set-up.
16: [----------] 6 tests from ThreadAffinityMultiRankTest
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
16: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (58 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
16: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (6 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
16: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (4 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
16: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (3 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
16: [----------] 6 tests from ThreadAffinityMultiRankTest (77 ms total)
16:
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (5 ms)
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (32 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 13 tests from 2 test cases ran. (109 ms total)
16: [ PASSED ] 13 tests.
16/52 Test #16: MdrunUtilityMpiUnitTests ............ Passed 0.17 sec
test 17
Start 17: MDSpanTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 32 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from BasicAccessorPolicy
17: [ RUN ] BasicAccessorPolicy.Decay
17: [ OK ] BasicAccessorPolicy.Decay (0 ms)
17: [ RUN ] BasicAccessorPolicy.Access
17: [ OK ] BasicAccessorPolicy.Access (0 ms)
17: [ RUN ] BasicAccessorPolicy.Offset
17: [ OK ] BasicAccessorPolicy.Offset (1 ms)
17: [ RUN ] BasicAccessorPolicy.CopyAccessor
17: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
17: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
17:
17: [----------] 4 tests from ExtentsTest
17: [ RUN ] ExtentsTest.Construction
17: [ OK ] ExtentsTest.Construction (0 ms)
17: [ RUN ] ExtentsTest.PurelyStatic
17: [ OK ] ExtentsTest.PurelyStatic (0 ms)
17: [ RUN ] ExtentsTest.RankNought
17: [ OK ] ExtentsTest.RankNought (0 ms)
17: [ RUN ] ExtentsTest.Assignment
17: [ OK ] ExtentsTest.Assignment (0 ms)
17: [----------] 4 tests from ExtentsTest (0 ms total)
17:
17: [----------] 8 tests from MdSpanExtension
17: [ RUN ] MdSpanExtension.SlicingAllStatic
17: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingDynamic
17: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingAllStatic3D
17: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
17: [ RUN ] MdSpanExtension.SlicingEqualsView3D
17: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
17: [ RUN ] MdSpanExtension.additionWorks
17: [ OK ] MdSpanExtension.additionWorks (0 ms)
17: [ RUN ] MdSpanExtension.subtractionWorks
17: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
17: [ RUN ] MdSpanExtension.multiplicationWorks
17: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
17: [ RUN ] MdSpanExtension.divisionWorks
17: [ OK ] MdSpanExtension.divisionWorks (0 ms)
17: [----------] 8 tests from MdSpanExtension (1 ms total)
17:
17: [----------] 3 tests from LayoutTests
17: [ RUN ] LayoutTests.LayoutRightConstruction
17: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
17: [ RUN ] LayoutTests.LayoutRightProperties
17: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
17: [ RUN ] LayoutTests.LayoutRightOperator
17: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
17: [----------] 3 tests from LayoutTests (0 ms total)
17:
17: [----------] 1 test from MdSpanTest
17: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
17: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
17: [----------] 1 test from MdSpanTest (0 ms total)
17:
17: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
17: [ RUN ] MdSpanTest/0.Rank
17: [ OK ] MdSpanTest/0.Rank (0 ms)
17: [ RUN ] MdSpanTest/0.DynamicRank
17: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/0.Extents
17: [ OK ] MdSpanTest/0.Extents (0 ms)
17: [ RUN ] MdSpanTest/0.Strides
17: [ OK ] MdSpanTest/0.Strides (0 ms)
17: [ RUN ] MdSpanTest/0.Properties
17: [ OK ] MdSpanTest/0.Properties (0 ms)
17: [ RUN ] MdSpanTest/0.Operator
17: [ OK ] MdSpanTest/0.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/0 (0 ms total)
17:
17: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
17: [ RUN ] MdSpanTest/1.Rank
17: [ OK ] MdSpanTest/1.Rank (0 ms)
17: [ RUN ] MdSpanTest/1.DynamicRank
17: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/1.Extents
17: [ OK ] MdSpanTest/1.Extents (0 ms)
17: [ RUN ] MdSpanTest/1.Strides
17: [ OK ] MdSpanTest/1.Strides (0 ms)
17: [ RUN ] MdSpanTest/1.Properties
17: [ OK ] MdSpanTest/1.Properties (0 ms)
17: [ RUN ] MdSpanTest/1.Operator
17: [ OK ] MdSpanTest/1.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/1 (1 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 32 tests from 7 test cases ran. (3 ms total)
17: [ PASSED ] 32 tests.
17/52 Test #17: MDSpanTests ......................... Passed 0.08 sec
test 18
Start 18: OnlineHelpUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 22 tests from 4 test cases.
18: [----------] Global test environment set-up.
18: [----------] 6 tests from TextTableFormatterTest
18: [ RUN ] TextTableFormatterTest.HandlesBasicCase
18: [ OK ] TextTableFormatterTest.HandlesBasicCase (5 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesIndentation
18: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
18: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (2 ms)
18: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
18: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
18: [----------] 6 tests from TextTableFormatterTest (12 ms total)
18:
18: [----------] 3 tests from HelpManagerTest
18: [ RUN ] HelpManagerTest.HandlesRootTopic
18: [ OK ] HelpManagerTest.HandlesRootTopic (2 ms)
18: [ RUN ] HelpManagerTest.HandlesSubTopics
18: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms)
18: [ RUN ] HelpManagerTest.HandlesInvalidTopics
18: [ OK ] HelpManagerTest.HandlesInvalidTopics (2 ms)
18: [----------] 3 tests from HelpManagerTest (5 ms total)
18:
18: [----------] 2 tests from HelpTopicFormattingTest
18: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
18: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (2 ms)
18: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
18: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
18: [----------] 2 tests from HelpTopicFormattingTest (3 ms total)
18:
18: [----------] 11 tests from HelpWriterContextTest
18: [ RUN ] HelpWriterContextTest.FormatsParagraphs
18: [ OK ] HelpWriterContextTest.FormatsParagraphs (2 ms)
18: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
18: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
18: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
18: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (2 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralText
18: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsBulletList
18: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
18: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
18: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsGridTable
18: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsTitles
18: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms)
18: [----------] 11 tests from HelpWriterContextTest (10 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 22 tests from 4 test cases ran. (30 ms total)
18: [ PASSED ] 22 tests.
18/52 Test #18: OnlineHelpUnitTests ................. Passed 0.09 sec
test 19
Start 19: OptionsUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 110 tests from 18 test cases.
19: [----------] Global test environment set-up.
19: [----------] 5 tests from AbstractOptionStorageTest
19: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
19: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
19: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (2 ms)
19: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
19: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
19: [----------] 5 tests from AbstractOptionStorageTest (4 ms total)
19:
19: [----------] 8 tests from FileNameOptionTest
19: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
19: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
19: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (1 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
19: [----------] 8 tests from FileNameOptionTest (2 ms total)
19:
19: [----------] 15 tests from FileNameOptionManagerTest
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (1 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
19: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
19: [----------] 15 tests from FileNameOptionManagerTest (5 ms total)
19:
19: [----------] 1 test from OptionsTest
19: [ RUN ] OptionsTest.FailsOnNonsafeStorage
19: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
19: [----------] 1 test from OptionsTest (0 ms total)
19:
19: [----------] 9 tests from OptionsAssignerTest
19: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
19: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
19: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (1 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMissingValue
19: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesExtraValue
19: [ OK ] OptionsAssignerTest.HandlesExtraValue (1 ms)
19: [ RUN ] OptionsAssignerTest.HandlesGroups
19: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesSections
19: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
19: [ OK ] OptionsAssignerTest.HandlesMultipleSources (1 ms)
19: [----------] 9 tests from OptionsAssignerTest (3 ms total)
19:
19: [----------] 4 tests from OptionsAssignerBooleanTest
19: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
19: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
19: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (1 ms)
19: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
19: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
19: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
19: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
19:
19: [----------] 13 tests from OptionsAssignerIntegerTest
19: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
19: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (1 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
19: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
19: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
19: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
19: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (1 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (1 ms)
19: [----------] 13 tests from OptionsAssignerIntegerTest (5 ms total)
19:
19: [----------] 5 tests from OptionsAssignerDoubleTest
19: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
19: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
19: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
19: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
19:
19: [----------] 9 tests from OptionsAssignerStringTest
19: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
19: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
19: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (1 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 9 tests from OptionsAssignerStringTest (2 ms total)
19:
19: [----------] 6 tests from OptionsAssignerEnumTest
19: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
19: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (1 ms)
19: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
19: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
19: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
19:
19: [----------] 8 tests from RepeatingOptionSectionTest
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (1 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
19: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
19: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
19: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
19: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
19:
19: [----------] 1 test from TimeUnitManagerTest
19: [ RUN ] TimeUnitManagerTest.BasicOperations
19: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
19: [----------] 1 test from TimeUnitManagerTest (0 ms total)
19:
19: [----------] 4 tests from TimeUnitBehaviorTest
19: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
19: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
19: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (1 ms)
19: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
19: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
19: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
19: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
19:
19: [----------] 2 tests from TreeValueSupportAssignTest
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
19: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
19:
19: [----------] 1 test from TreeValueSupportAssignErrorTest
19: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
19: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
19: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
19:
19: [----------] 5 tests from TreeValueSupportCheckTest
19: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
19: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
19: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
19: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
19: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
19:
19: [----------] 6 tests from TreeValueSupportAdjustTest
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (4 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
19: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
19: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
19: [----------] 6 tests from TreeValueSupportAdjustTest (9 ms total)
19:
19: [----------] 8 tests from TreeValueSupportTest
19: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
19: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
19: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsInt64Option
19: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsStringOption
19: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsFloatOption
19: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
19: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
19: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumOption
19: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
19: [----------] 8 tests from TreeValueSupportTest (9 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 110 tests from 18 test cases ran. (49 ms total)
19: [ PASSED ] 110 tests.
19/52 Test #19: OptionsUnitTests .................... Passed 0.13 sec
test 20
Start 20: PbcutilUnitTest
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 2 test cases.
20: [----------] Global test environment set-up.
20: [----------] 1 test from PbcTest
20: [ RUN ] PbcTest.CalcShiftsWorks
20: [ OK ] PbcTest.CalcShiftsWorks (17 ms)
20: [----------] 1 test from PbcTest (18 ms total)
20:
20: [----------] 2 tests from PbcEnumsTest
20: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
20: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
20: [----------] 2 tests from PbcEnumsTest (0 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 2 test cases ran. (20 ms total)
20: [ PASSED ] 3 tests.
20/52 Test #20: PbcutilUnitTest ..................... Passed 0.08 sec
test 21
Start 21: RandomUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 44 tests from 10 test cases.
21: [----------] Global test environment set-up.
21: [----------] 4 tests from ExponentialDistributionTest
21: [ RUN ] ExponentialDistributionTest.Output
21: [ OK ] ExponentialDistributionTest.Output (1 ms)
21: [ RUN ] ExponentialDistributionTest.Logical
21: [ OK ] ExponentialDistributionTest.Logical (0 ms)
21: [ RUN ] ExponentialDistributionTest.Reset
21: [ OK ] ExponentialDistributionTest.Reset (0 ms)
21: [ RUN ] ExponentialDistributionTest.AltParam
21: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from ExponentialDistributionTest (2 ms total)
21:
21: [----------] 4 tests from GammaDistributionTest
21: [ RUN ] GammaDistributionTest.Output
21: [ OK ] GammaDistributionTest.Output (1 ms)
21: [ RUN ] GammaDistributionTest.Logical
21: [ OK ] GammaDistributionTest.Logical (0 ms)
21: [ RUN ] GammaDistributionTest.Reset
21: [ OK ] GammaDistributionTest.Reset (0 ms)
21: [ RUN ] GammaDistributionTest.AltParam
21: [ OK ] GammaDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from GammaDistributionTest (2 ms total)
21:
21: [----------] 4 tests from NormalDistributionTest
21: [ RUN ] NormalDistributionTest.Output
21: [ OK ] NormalDistributionTest.Output (1 ms)
21: [ RUN ] NormalDistributionTest.Logical
21: [ OK ] NormalDistributionTest.Logical (0 ms)
21: [ RUN ] NormalDistributionTest.Reset
21: [ OK ] NormalDistributionTest.Reset (0 ms)
21: [ RUN ] NormalDistributionTest.AltParam
21: [ OK ] NormalDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from NormalDistributionTest (2 ms total)
21:
21: [----------] 1 test from SeedTest
21: [ RUN ] SeedTest.makeRandomSeed
21: [ OK ] SeedTest.makeRandomSeed (12 ms)
21: [----------] 1 test from SeedTest (13 ms total)
21:
21: [----------] 6 tests from TabulatedNormalDistributionTest
21: [ RUN ] TabulatedNormalDistributionTest.Output14
21: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Output16
21: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
21: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Logical
21: [ OK ] TabulatedNormalDistributionTest.Logical (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Reset
21: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.AltParam
21: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
21: [----------] 6 tests from TabulatedNormalDistributionTest (3 ms total)
21:
21: [----------] 1 test from TabulatedNormalDistributionTableTest
21: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
21: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (9 ms)
21: [----------] 1 test from TabulatedNormalDistributionTableTest (9 ms total)
21:
21: [----------] 6 tests from ThreeFry2x64Test
21: [ RUN ] ThreeFry2x64Test.Logical
21: [ OK ] ThreeFry2x64Test.Logical (0 ms)
21: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
21: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
21: [ RUN ] ThreeFry2x64Test.Reseed
21: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
21: [ RUN ] ThreeFry2x64Test.Discard
21: [ OK ] ThreeFry2x64Test.Discard (0 ms)
21: [ RUN ] ThreeFry2x64Test.InvalidCounter
21: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
21: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
21: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (1 ms)
21: [----------] 6 tests from ThreeFry2x64Test (3 ms total)
21:
21: [----------] 4 tests from UniformIntDistributionTest
21: [ RUN ] UniformIntDistributionTest.Output
21: [ OK ] UniformIntDistributionTest.Output (1 ms)
21: [ RUN ] UniformIntDistributionTest.Logical
21: [ OK ] UniformIntDistributionTest.Logical (0 ms)
21: [ RUN ] UniformIntDistributionTest.Reset
21: [ OK ] UniformIntDistributionTest.Reset (0 ms)
21: [ RUN ] UniformIntDistributionTest.AltParam
21: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
21:
21: [----------] 5 tests from UniformRealDistributionTest
21: [ RUN ] UniformRealDistributionTest.GenerateCanonical
21: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
21: [ RUN ] UniformRealDistributionTest.Output
21: [ OK ] UniformRealDistributionTest.Output (1 ms)
21: [ RUN ] UniformRealDistributionTest.Logical
21: [ OK ] UniformRealDistributionTest.Logical (0 ms)
21: [ RUN ] UniformRealDistributionTest.Reset
21: [ OK ] UniformRealDistributionTest.Reset (0 ms)
21: [ RUN ] UniformRealDistributionTest.AltParam
21: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
21: [----------] 5 tests from UniformRealDistributionTest (3 ms total)
21:
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (6 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 44 tests from 10 test cases ran. (45 ms total)
21: [ PASSED ] 44 tests.
21/52 Test #21: RandomUnitTests ..................... Passed 0.15 sec
test 22
Start 22: RestraintTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 1 test from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 1 test from RestraintManager
22: [ RUN ] RestraintManager.restraintList
22: [ OK ] RestraintManager.restraintList (0 ms)
22: [----------] 1 test from RestraintManager (0 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 1 test from 1 test case ran. (1 ms total)
22: [ PASSED ] 1 test.
22/52 Test #22: RestraintTests ...................... Passed 0.06 sec
test 23
Start 23: TableUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 16 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
23: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectInput (7 ms)
23: [ RUN ] SplineTableTest/0.Sinc
23: [ OK ] SplineTableTest/0.Sinc (4 ms)
23: [ RUN ] SplineTableTest/0.LJ12
23: [ OK ] SplineTableTest/0.LJ12 (80 ms)
23: [ RUN ] SplineTableTest/0.PmeCorrection
23: [ OK ] SplineTableTest/0.PmeCorrection (7 ms)
23: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
23: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms)
23: [ RUN ] SplineTableTest/0.TwoFunctions
23: [ OK ] SplineTableTest/0.TwoFunctions (164 ms)
23: [ RUN ] SplineTableTest/0.ThreeFunctions
23: [ OK ] SplineTableTest/0.ThreeFunctions (188 ms)
23: [----------] 8 tests from SplineTableTest/0 (458 ms total)
23:
23: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
23: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
23: [ RUN ] SplineTableTest/1.Sinc
23: [ OK ] SplineTableTest/1.Sinc (3 ms)
23: [ RUN ] SplineTableTest/1.LJ12
23: [ OK ] SplineTableTest/1.LJ12 (11 ms)
23: [ RUN ] SplineTableTest/1.PmeCorrection
23: [ OK ] SplineTableTest/1.PmeCorrection (7 ms)
23: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
23: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms)
23: [ RUN ] SplineTableTest/1.TwoFunctions
23: [ OK ] SplineTableTest/1.TwoFunctions (23 ms)
23: [ RUN ] SplineTableTest/1.ThreeFunctions
23: [ OK ] SplineTableTest/1.ThreeFunctions (26 ms)
23: [----------] 8 tests from SplineTableTest/1 (88 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 16 tests from 2 test cases ran. (547 ms total)
23: [ PASSED ] 16 tests.
23/52 Test #23: TableUnitTests ...................... Passed 0.61 sec
test 24
Start 24: TaskAssignmentUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 3 tests from 2 test cases.
24: [----------] Global test environment set-up.
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
24: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
24: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (2 ms)
24: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
24: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
24: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
24: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 3 tests from 2 test cases ran. (4 ms total)
24: [ PASSED ] 3 tests.
24/52 Test #24: TaskAssignmentUnitTests ............. Passed 0.07 sec
test 25
Start 25: TopologyTest
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 11 tests from 3 test cases.
25: [----------] Global test environment set-up.
25: [----------] 3 tests from ExclusionBlockTest
25: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
25: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
25: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
25: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
25: [ RUN ] ExclusionBlockTest.MergeExclusions
25: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
25: [----------] 3 tests from ExclusionBlockTest (0 ms total)
25:
25: [----------] 2 tests from MtopTest
25: [ RUN ] MtopTest.RangeBasedLoop
25: [ OK ] MtopTest.RangeBasedLoop (1 ms)
25: [ RUN ] MtopTest.Operators
25: [ OK ] MtopTest.Operators (0 ms)
25: [----------] 2 tests from MtopTest (1 ms total)
25:
25: [----------] 6 tests from SymtabTest
25: [ RUN ] SymtabTest.EmptyOnOpen
25: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
25: [ RUN ] SymtabTest.AddSingleEntry
25: [ OK ] SymtabTest.AddSingleEntry (0 ms)
25: [ RUN ] SymtabTest.AddTwoDistinctEntries
25: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
25: [ RUN ] SymtabTest.TryToAddDuplicates
25: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
25: [ RUN ] SymtabTest.AddLargeNumberOfEntries
25: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms)
25: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
25: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms)
25: [----------] 6 tests from SymtabTest (2 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 11 tests from 3 test cases ran. (3 ms total)
25: [ PASSED ] 11 tests.
25/52 Test #25: TopologyTest ........................ Passed 0.07 sec
test 26
Start 26: PullTest
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 5 tests from 1 test case.
26: [----------] Global test environment set-up.
26: [----------] 5 tests from PullTest
26: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
26: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
26: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
26: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
26: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
26: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
26: [----------] 5 tests from PullTest (0 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 5 tests from 1 test case ran. (1 ms total)
26: [ PASSED ] 5 tests.
26/52 Test #26: PullTest ............................ Passed 0.06 sec
test 27
Start 27: AwhTest
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
27: Test timeout computed to be: 30
27: [==========] Running 12 tests from 4 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from BiasTest
27: [ RUN ] BiasTest.DetectsCovering
27: [ OK ] BiasTest.DetectsCovering (3 ms)
27: [----------] 1 test from BiasTest (3 ms total)
27:
27: [----------] 1 test from gridTest
27: [ RUN ] gridTest.neighborhood
27: [ OK ] gridTest.neighborhood (9 ms)
27: [----------] 1 test from gridTest (9 ms total)
27:
27: [----------] 8 tests from WithParameters/BiasTest
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (43 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (9 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (3 ms)
27: [----------] 8 tests from WithParameters/BiasTest (71 ms total)
27:
27: [----------] 2 tests from WithParameters/BiasStateTest
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (2 ms)
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
27: [----------] 2 tests from WithParameters/BiasStateTest (4 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 12 tests from 4 test cases ran. (88 ms total)
27: [ PASSED ] 12 tests.
27/52 Test #27: AwhTest ............................. Passed 0.15 sec
test 28
Start 28: SimdUnitTests
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 86 tests from 3 test cases.
28: [----------] Global test environment set-up.
28: [----------] 41 tests from SimdScalarTest
28: [ RUN ] SimdScalarTest.load
28: [ OK ] SimdScalarTest.load (0 ms)
28: [ RUN ] SimdScalarTest.loadU
28: [ OK ] SimdScalarTest.loadU (0 ms)
28: [ RUN ] SimdScalarTest.store
28: [ OK ] SimdScalarTest.store (0 ms)
28: [ RUN ] SimdScalarTest.storeU
28: [ OK ] SimdScalarTest.storeU (0 ms)
28: [ RUN ] SimdScalarTest.setZero
28: [ OK ] SimdScalarTest.setZero (0 ms)
28: [ RUN ] SimdScalarTest.andNot
28: [ OK ] SimdScalarTest.andNot (0 ms)
28: [ RUN ] SimdScalarTest.fma
28: [ OK ] SimdScalarTest.fma (0 ms)
28: [ RUN ] SimdScalarTest.fms
28: [ OK ] SimdScalarTest.fms (0 ms)
28: [ RUN ] SimdScalarTest.fnma
28: [ OK ] SimdScalarTest.fnma (0 ms)
28: [ RUN ] SimdScalarTest.fnms
28: [ OK ] SimdScalarTest.fnms (0 ms)
28: [ RUN ] SimdScalarTest.maskAdd
28: [ OK ] SimdScalarTest.maskAdd (0 ms)
28: [ RUN ] SimdScalarTest.maskzMul
28: [ OK ] SimdScalarTest.maskzMul (0 ms)
28: [ RUN ] SimdScalarTest.maskzFma
28: [ OK ] SimdScalarTest.maskzFma (0 ms)
28: [ RUN ] SimdScalarTest.abs
28: [ OK ] SimdScalarTest.abs (0 ms)
28: [ RUN ] SimdScalarTest.max
28: [ OK ] SimdScalarTest.max (0 ms)
28: [ RUN ] SimdScalarTest.min
28: [ OK ] SimdScalarTest.min (0 ms)
28: [ RUN ] SimdScalarTest.round
28: [ OK ] SimdScalarTest.round (0 ms)
28: [ RUN ] SimdScalarTest.trunc
28: [ OK ] SimdScalarTest.trunc (0 ms)
28: [ RUN ] SimdScalarTest.reduce
28: [ OK ] SimdScalarTest.reduce (0 ms)
28: [ RUN ] SimdScalarTest.testBits
28: [ OK ] SimdScalarTest.testBits (0 ms)
28: [ RUN ] SimdScalarTest.anyTrue
28: [ OK ] SimdScalarTest.anyTrue (0 ms)
28: [ RUN ] SimdScalarTest.selectByMask
28: [ OK ] SimdScalarTest.selectByMask (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMask
28: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
28: [ RUN ] SimdScalarTest.blend
28: [ OK ] SimdScalarTest.blend (0 ms)
28: [ RUN ] SimdScalarTest.cvtR2I
28: [ OK ] SimdScalarTest.cvtR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvttR2I
28: [ OK ] SimdScalarTest.cvttR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvtI2R
28: [ OK ] SimdScalarTest.cvtI2R (0 ms)
28: [ RUN ] SimdScalarTest.cvtF2D
28: [ OK ] SimdScalarTest.cvtF2D (0 ms)
28: [ RUN ] SimdScalarTest.cvtD2D
28: [ OK ] SimdScalarTest.cvtD2D (0 ms)
28: [ RUN ] SimdScalarTest.loadI
28: [ OK ] SimdScalarTest.loadI (0 ms)
28: [ RUN ] SimdScalarTest.loadUI
28: [ OK ] SimdScalarTest.loadUI (0 ms)
28: [ RUN ] SimdScalarTest.storeI
28: [ OK ] SimdScalarTest.storeI (0 ms)
28: [ RUN ] SimdScalarTest.storeUI
28: [ OK ] SimdScalarTest.storeUI (0 ms)
28: [ RUN ] SimdScalarTest.andNotI
28: [ OK ] SimdScalarTest.andNotI (0 ms)
28: [ RUN ] SimdScalarTest.testBitsI
28: [ OK ] SimdScalarTest.testBitsI (0 ms)
28: [ RUN ] SimdScalarTest.selectByMaskI
28: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMaskI
28: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
28: [ RUN ] SimdScalarTest.blendI
28: [ OK ] SimdScalarTest.blendI (0 ms)
28: [ RUN ] SimdScalarTest.cvtB2IB
28: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
28: [ RUN ] SimdScalarTest.cvtIB2B
28: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
28: [ RUN ] SimdScalarTest.expandScalarsToTriplets
28: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
28: [----------] 41 tests from SimdScalarTest (2 ms total)
28:
28: [----------] 8 tests from SimdScalarUtilTest
28: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
28: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
28: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
28: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
28: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
28: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
28:
28: [----------] 37 tests from SimdScalarMathTest
28: [ RUN ] SimdScalarMathTest.copysign
28: [ OK ] SimdScalarMathTest.copysign (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPair
28: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
28: [ RUN ] SimdScalarMathTest.inv
28: [ OK ] SimdScalarMathTest.inv (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrt
28: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
28: [ RUN ] SimdScalarMathTest.log
28: [ OK ] SimdScalarMathTest.log (0 ms)
28: [ RUN ] SimdScalarMathTest.exp2
28: [ OK ] SimdScalarMathTest.exp2 (0 ms)
28: [ RUN ] SimdScalarMathTest.exp
28: [ OK ] SimdScalarMathTest.exp (0 ms)
28: [ RUN ] SimdScalarMathTest.erf
28: [ OK ] SimdScalarMathTest.erf (0 ms)
28: [ RUN ] SimdScalarMathTest.erfc
28: [ OK ] SimdScalarMathTest.erfc (0 ms)
28: [ RUN ] SimdScalarMathTest.sincos
28: [ OK ] SimdScalarMathTest.sincos (0 ms)
28: [ RUN ] SimdScalarMathTest.sin
28: [ OK ] SimdScalarMathTest.sin (0 ms)
28: [ RUN ] SimdScalarMathTest.cos
28: [ OK ] SimdScalarMathTest.cos (0 ms)
28: [ RUN ] SimdScalarMathTest.tan
28: [ OK ] SimdScalarMathTest.tan (0 ms)
28: [ RUN ] SimdScalarMathTest.asin
28: [ OK ] SimdScalarMathTest.asin (0 ms)
28: [ RUN ] SimdScalarMathTest.acos
28: [ OK ] SimdScalarMathTest.acos (0 ms)
28: [ RUN ] SimdScalarMathTest.atan
28: [ OK ] SimdScalarMathTest.atan (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2
28: [ OK ] SimdScalarMathTest.atan2 (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrection
28: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
28: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
28: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.invSingleAccuracy
28: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
28: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.logSingleAccuracy
28: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
28: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.expSingleAccuracy
28: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
28: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
28: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
28: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
28: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
28: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
28: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
28: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
28: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
28: [----------] 37 tests from SimdScalarMathTest (2 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 86 tests from 3 test cases ran. (4 ms total)
28: [ PASSED ] 86 tests.
28/52 Test #28: SimdUnitTests ....................... Passed 0.08 sec
test 29
Start 29: CompatibilityHelpersTests
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 170 tests from 12 test cases.
29: [----------] Global test environment set-up.
29: [----------] 45 tests from OptionalTest
29: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
29: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructEmpty
29: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
29: [ RUN ] OptionalTest.CanConstructFromNullopt
29: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
29: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
29: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
29: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValue
29: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
29: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValue
29: [ OK ] OptionalTest.CanMoveConstructFromValue (1 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
29: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
29: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
29: [ OK ] OptionalTest.CanCopyAssignFromLiteral (1 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromValue
29: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanMoveAssignFromValue
29: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanResetContent
29: [ OK ] OptionalTest.CanResetContent (0 ms)
29: [ RUN ] OptionalTest.ProvidesRelationalOperators
29: [ OK ] OptionalTest.ProvidesRelationalOperators (1 ms)
29: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
29: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms)
29: [ RUN ] OptionalTest.CanProduceHash
29: [ OK ] OptionalTest.CanProduceHash (0 ms)
29: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
29: alignment_of<char>: 1
29: alignment_of<short>: 2
29: alignment_of<int>: 4
29: alignment_of<long>: 4
29: alignment_of<float>: 4
29: alignment_of<double>: 8
29: alignment_of<long double>: 8
29: alignment_of<Struct>: 1
29: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
29: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
29: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
29: sizeof( optional<char> ): 2 (1)
29: sizeof( optional<short> ): 4 (2)
29: sizeof( optional<int> ): 8 (4)
29: sizeof( optional<long> ): 8 (4)
29: sizeof( optional<float> ): 8 (4)
29: sizeof( optional<double> ): 16 (8)
29: sizeof( optional<long double> ): 16 (8)
29: sizeof( optional<Struct> ): 2 (1)
29: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
29: [----------] 45 tests from OptionalTest (4 ms total)
29:
29: [----------] 7 tests from MakeOptionalTest
29: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (1 ms)
29: [ RUN ] MakeOptionalTest.CanCopyConstruct
29: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanMoveConstruct
29: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
29: [----------] 7 tests from MakeOptionalTest (1 ms total)
29:
29: [----------] 4 tests from OptionalMemberSwapTest
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
29: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
29:
29: [----------] 4 tests from OptionalImplicitValueTest
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
29: [----------] 4 tests from OptionalImplicitValueTest (1 ms total)
29:
29: [----------] 20 tests from OptionalIntValueTest
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
29: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (1 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
29: [----------] 20 tests from OptionalIntValueTest (2 ms total)
29:
29: [----------] 1 test from NotNullConstruction
29: [ RUN ] NotNullConstruction.Works
29: [ OK ] NotNullConstruction.Works (0 ms)
29: [----------] 1 test from NotNullConstruction (0 ms total)
29:
29: [----------] 1 test from NotNullCasting
29: [ RUN ] NotNullCasting.Works
29: [ OK ] NotNullCasting.Works (0 ms)
29: [----------] 1 test from NotNullCasting (0 ms total)
29:
29: [----------] 1 test from NotNullAssignment
29: [ RUN ] NotNullAssignment.Works
29: [ OK ] NotNullAssignment.Works (0 ms)
29: [----------] 1 test from NotNullAssignment (0 ms total)
29:
29: [----------] 1 test from MakeNotNull
29: [ RUN ] MakeNotNull.Works
29: [ OK ] MakeNotNull.Works (0 ms)
29: [----------] 1 test from MakeNotNull (0 ms total)
29:
29: [----------] 1 test from NotNull
29: [ RUN ] NotNull.WorksInContainers
29: [ OK ] NotNull.WorksInContainers (0 ms)
29: [----------] 1 test from NotNull (0 ms total)
29:
29: [----------] 80 tests from StringViewTest
29: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
29: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
29: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
29: [ RUN ] StringViewTest.CanConstructFromCString
29: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
29: [ RUN ] StringViewTest.AllowForwardIteration
29: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstForwardIteration
29: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowReverseIteration
29: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstReverseIteration
29: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
29: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
29: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
29: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
29: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
29: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaAt
29: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
29: [ RUN ] StringViewTest.CanAccessAllElementsViaData
29: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
29: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
29: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
29: [ RUN ] StringViewTest.CanRemovePrefix
29: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
29: [ RUN ] StringViewTest.CanRemoveSuffix
29: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
29: [ RUN ] StringViewTest.CanSwapWithOtherView
29: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
29: [ RUN ] StringViewTest.CanCopySubstringWithCopy
29: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
29: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
29: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
29: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
29: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
29: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCompareToViews
29: [ OK ] StringViewTest.CanCompareToViews (0 ms)
29: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
29: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
29: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
29: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
29: [ RUN ] StringViewTest.CanPrintViewToPutputStream
29: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
29: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
29: [----------] 80 tests from StringViewTest (6 ms total)
29:
29: [----------] 5 tests from StringViewExtensionTest
29: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
29: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (1 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
29: [----------] 5 tests from StringViewExtensionTest (1 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 170 tests from 12 test cases ran. (16 ms total)
29: [ PASSED ] 170 tests.
29/52 Test #29: CompatibilityHelpersTests ........... Passed 0.10 sec
test 30
Start 30: GmxAnaTest
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
30: Test timeout computed to be: 600
30: [==========] Running 27 tests from 5 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from Entropy
30: [ RUN ] Entropy.Schlitter_300_NoLinear
30: [ OK ] Entropy.Schlitter_300_NoLinear (60 ms)
30: [ RUN ] Entropy.Schlitter_300_Linear
30: [ OK ] Entropy.Schlitter_300_Linear (56 ms)
30: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (1 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_Linear
30: [ OK ] Entropy.QuasiHarmonic_200_Linear (9 ms)
30: [----------] 5 tests from Entropy (126 ms total)
30:
30: [----------] 10 tests from MindistTest
30: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistWorksWithSingleAtoms (32 ms)
30: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (5 ms)
30: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms)
30: [ RUN ] MindistTest.mindistPicksUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistPicksUpContacts (6 ms)
30: [ RUN ] MindistTest.ngWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.ngWorks (5 ms)
30: [ RUN ] MindistTest.groupWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.groupWorks (6 ms)
30: [ RUN ] MindistTest.maxDistWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.maxDistWorks (15 ms)
30: [ RUN ] MindistTest.noPbcWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.noPbcWorks (5 ms)
30: [ RUN ] MindistTest.resPerTimeWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.resPerTimeWorks (5 ms)
30: [ RUN ] MindistTest.matrixWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 5: 'atoms123'
30: Special case: making distance matrix between all atoms in group atoms123
30: [ OK ] MindistTest.matrixWorks (5 ms)
30: [----------] 10 tests from MindistTest (90 ms total)
30:
30: [----------] 3 tests from MsdTest
30: [ RUN ] MsdTest.threeDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.threeDimensionalDiffusion (5 ms)
30: [ RUN ] MsdTest.twoDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.twoDimensionalDiffusion (5 ms)
30: [ RUN ] MsdTest.oneDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.oneDimensionalDiffusion (5 ms)
30: [----------] 3 tests from MsdTest (16 ms total)
30:
30: [----------] 3 tests from MsdMolTest
30: [ RUN ] MsdMolTest.diffMolMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -1095967172
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolMassWeighted (3216 ms)
30: [ RUN ] MsdMolTest.diffMolNonMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 443802500
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolNonMassWeighted (3117 ms)
30: [ RUN ] MsdMolTest.diffMolSelected
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -44025615
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( mol) has 9 elements
30: There is one group in the index
30: Split group of 9 atoms into 3 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolSelected (3133 ms)
30: [----------] 3 tests from MsdMolTest (9467 ms total)
30:
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: trr version: GMX_trn_file (single precision)
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (25 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (10 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (8 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from gro file '', 6 atoms.
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (16 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
30:
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (8 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (14 ms)
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (82 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 27 tests from 5 test cases ran. (9783 ms total)
30: [ PASSED ] 27 tests.
30/52 Test #30: GmxAnaTest .......................... Passed 9.86 sec
test 31
Start 31: GmxPreprocessTests
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
31: Test timeout computed to be: 30
31: [==========] Running 68 tests from 9 test cases.
31: [----------] Global test environment set-up.
31: [----------] 4 tests from GenconfTest
31: [ RUN ] GenconfTest.nbox_Works
31: [ OK ] GenconfTest.nbox_Works (25 ms)
31: [ RUN ] GenconfTest.nbox_norenumber_Works
31: [ OK ] GenconfTest.nbox_norenumber_Works (15 ms)
31: [ RUN ] GenconfTest.nbox_dist_Works
31: [ OK ] GenconfTest.nbox_dist_Works (32 ms)
31: [ RUN ] GenconfTest.nbox_rot_Works
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: [ OK ] GenconfTest.nbox_rot_Works (9 ms)
31: [----------] 4 tests from GenconfTest (82 ms total)
31:
31: [----------] 2 tests from GenionTest
31: [ RUN ] GenionTest.HighConcentrationIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to 1010136221
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
31: Group 0 ( System) has 653 elements
31: Group 1 ( Water) has 648 elements
31: Group 2 ( SOL) has 648 elements
31: Group 3 ( non-Water) has 5 elements
31: Group 4 ( Other) has 5 elements
31: Group 5 ( METH) has 5 elements
31: Select a group: Number of (3-atomic) solvent molecules: 216
31: Using random seed 1997.
31: Replacing solvent molecule 56 (atom 168) with NA
31: Replacing solvent molecule 120 (atom 360) with NA
31: Replacing solvent molecule 182 (atom 546) with NA
31: Replacing solvent molecule 71 (atom 213) with NA
31: Replacing solvent molecule 189 (atom 567) with CL
31: Replacing solvent molecule 54 (atom 162) with CL
31: Replacing solvent molecule 155 (atom 465) with CL
31: Replacing solvent molecule 99 (atom 297) with CL
31:
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: Will try to add 4 NA ions and 4 CL ions.
31: Select a continuous group of solvent molecules
31: Selected 1: 'Water'
31: [ OK ] GenionTest.HighConcentrationIonPlacement (3250 ms)
31: [ RUN ] GenionTest.NoIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to 981580039
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
31: No ions to add, will just copy input configuration.
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: [ OK ] GenionTest.NoIonPlacement (3194 ms)
31: [----------] 2 tests from GenionTest (6446 ms total)
31:
31: [----------] 9 tests from PreprocessingAtomTypesTest
31: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
31: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
31: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
31: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total)
31:
31: [----------] 10 tests from PreprocessingBondAtomTypeTest
31: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
31: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
31: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
31: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
31:
31: [----------] 5 tests from InsertMoleculesTest
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
31: Added 1 molecules (out of 1 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
31:
31: Output configuration contains 8 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (23 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3 success (now 6 atoms)!
31:
Try 4 success (now 8 atoms)!
31:
Try 5 success (now 10 atoms)!
31:
31: Added 5 molecules (out of 5 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
31:
31: Output configuration contains 10 atoms in 10 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (21 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
Try 2 success (now 10 atoms)!
31:
31: Added 2 molecules (out of 2 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
31:
31: Output configuration contains 10 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (12 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 650 atoms)!
31:
Try 2 success (now 652 atoms)!
31:
Try 3 success (now 654 atoms)!
31:
Try 4 success (now 656 atoms)!
31:
31: Added 4 molecules (out of 4 requested)
31: Replaced 8 residues (24 atoms)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
31:
31: Output configuration contains 632 atoms in 212 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (69 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
31:
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
31:
Try 13 success (now 6 atoms)!
31:
31: Added 3 molecules (out of 4 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
31:
31: Output configuration contains 6 atoms in 3 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (13 ms)
31: [----------] 5 tests from InsertMoleculesTest (142 ms total)
31:
31: [----------] 14 tests from GetIrTest
31: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
31: Ignoring obsolete mdp entry 'title'
31: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (27 ms)
31: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
31: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (29 ms)
31: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsKeyWithoutValue (23 ms)
31: [ RUN ] GetIrTest.RejectsValueWithoutKey
31: [ OK ] GetIrTest.RejectsValueWithoutKey (29 ms)
31: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
31: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (30 ms)
31: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (23 ms)
31: [ RUN ] GetIrTest.AcceptsEmptyLines
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsEmptyLines (19 ms)
31: [ RUN ] GetIrTest.AcceptsElectricField
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricField (59 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (43 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (30 ms)
31: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
31: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (12 ms)
31: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsImplicitSolventNo (30 ms)
31: [ RUN ] GetIrTest.RejectsImplicitSolventYes
31: [ OK ] GetIrTest.RejectsImplicitSolventYes (29 ms)
31: [ RUN ] GetIrTest.AcceptsMimic
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsMimic (34 ms)
31: [----------] 14 tests from GetIrTest (418 ms total)
31:
31: [----------] 5 tests from SolvateTest
31: [ RUN ] SolvateTest.cs_box_Works
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 1x1x1 boxes
31: Solvent box contains 270 atoms in 90 residues
31: Removed 129 solvent atoms due to solvent-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 47 residues
31: Generated solvent containing 141 atoms in 47 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
31:
31: Output configuration contains 141 atoms in 47 residues
31: Volume : 1.331 (nm^3)
31: Density : 1056.36 (g/l)
31: Number of solvent molecules: 47
31:
31: [ OK ] SolvateTest.cs_box_Works (86 ms)
31: [ RUN ] SolvateTest.cs_cp_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: [ OK ] SolvateTest.cs_cp_Works (279 ms)
31: [ RUN ] SolvateTest.cs_cp_p_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: Processing topology
31: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
31: [ OK ] SolvateTest.cs_cp_p_Works (281 ms)
31: [ RUN ] SolvateTest.shell_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 1902 solvent atoms more than 1.000000 nm from solute.
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 252 residues
31: Generated solvent containing 756 atoms in 252 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
31:
31: Output configuration contains 762 atoms in 254 residues
31: Volume : 27.2709 (nm^3)
31: Density : 279.3 (g/l)
31: Number of solvent molecules: 252
31:
31: [ OK ] SolvateTest.shell_Works (141 ms)
31: [ RUN ] SolvateTest.update_Topology_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 3x3x3 boxes
31: Solvent box contains 14952 atoms in 4984 residues
31: Removed 2787 solvent atoms due to solvent-solvent overlap
31: Removed 30 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 2 different molecule types:
31: HOH ( 3 atoms): 1876 residues
31: SOL ( 3 atoms): 2169 residues
31: Generated solvent containing 0 atoms in 0 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
31:
31: Output configuration contains 12141 atoms in 4047 residues
31: Volume : 125 (nm^3)
31: Density : 968.963 (g/l)
31: Number of solvent molecules: 4045
31:
31: Processing topology
31: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: [ OK ] SolvateTest.update_Topology_Works (1138 ms)
31: [----------] 5 tests from SolvateTest (1925 ms total)
31:
31: [----------] 1 test from TopDirTests
31: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
31: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
31: [----------] 1 test from TopDirTests (0 ms total)
31:
31: [----------] 18 tests from SinglePeptideFragments/EditconfTest
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (94 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (34 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (37 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (34 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (21 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (27 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (24 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (16 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (20 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (36 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (31 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (39 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (15 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (11 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (12 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (17 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (14 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (15 ms)
31: [----------] 18 tests from SinglePeptideFragments/EditconfTest (509 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 68 tests from 9 test cases ran. (9524 ms total)
31: [ PASSED ] 68 tests.
31/52 Test #31: GmxPreprocessTests .................. Passed 9.60 sec
test 32
Start 32: Pdb2gmx1Test
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 24 tests from 1 test case.
32: [----------] Global test environment set-up.
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (1031 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (604 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (530 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (476 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (566 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (658 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (577 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (509 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (743 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (596 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (670 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (489 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (562 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (600 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (652 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (524 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (523 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (610 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (531 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (503 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (557 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (621 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (580 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (518 ms)
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (14256 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 24 tests from 1 test case ran. (14259 ms total)
32: [ PASSED ] 24 tests.
32/52 Test #32: Pdb2gmx1Test ........................ Passed 14.33 sec
test 33
Start 33: Pdb2gmx2Test
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 32 tests from 2 test cases.
33: [----------] Global test environment set-up.
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (379 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (354 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (330 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (489 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (505 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (379 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (482 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (511 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (500 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (528 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (312 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (300 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (478 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (560 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (508 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (481 ms)
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (7100 ms total)
33:
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (576 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (414 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (351 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (507 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (752 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (416 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (491 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (577 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (345 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (559 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (353 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (334 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (441 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (402 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (430 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (406 ms)
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (7357 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 32 tests from 2 test cases ran. (14458 ms total)
33: [ PASSED ] 32 tests.
33/52 Test #33: Pdb2gmx2Test ........................ Passed 14.53 sec
test 34
Start 34: Pdb2gmx3Test
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
34: Test timeout computed to be: 30
34: [==========] Running 28 tests from 4 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (525 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (587 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (442 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (397 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (579 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (539 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (510 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (439 ms)
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (4021 ms total)
34:
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (440 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (493 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (439 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (404 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (471 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (659 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (504 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (433 ms)
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (3846 ms total)
34:
34: [----------] 8 tests from ChainSep/Pdb2gmxTest
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (458 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 7 acceptors were found.
34: There are 7 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS8
34: NE223
34: MET12 SD55 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 125, now 125
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 317 pairs
34: Before cleaning: 322 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 5 cmap torsion pairs
34: There are 322 dihedrals, 19 impropers, 227 angles
34: 314 pairs, 125 bonds and 0 virtual sites
34: Total mass 846.083 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 7 58
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (58 atoms, 7 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 7 residues with 124 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 124 atoms 7 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (295 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (450 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 12 acceptors were found.
34: There are 13 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3
34: SG9
34: HIS8 NE251 1.055
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 115, now 115
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 288 pairs
34: Before cleaning: 293 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 6 cmap torsion pairs
34: There are 293 dihedrals, 23 impropers, 203 angles
34: 285 pairs, 115 bonds and 0 virtual sites
34: Total mass 888.952 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 8 61
34: 2 'B' 3 25
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (61 atoms, 8 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 8 residues with 114 atoms
34: Chain time...
34: Processing chain 2 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 114 atoms 8 residues
34: Including chain 2 in system: 61 atoms 3 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (294 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 260, now 260
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 650 pairs
34: Before cleaning: 660 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 8 cmap torsion pairs
34: There are 660 dihedrals, 45 impropers, 466 angles
34: 647 pairs, 260 bonds and 0 virtual sites
34: Total mass 1900.162 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34:
34: Merged chains into joint molecule definitions at 3 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 261 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (439 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 6 donors and 4 acceptors were found.
34: There are 3 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 67, now 67
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 164 pairs
34: Before cleaning: 169 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 169 dihedrals, 13 impropers, 118 angles
34: 161 pairs, 67 bonds and 0 virtual sites
34: Total mass 472.547 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 261 atoms and 16 residues
34: Total mass in system 1900.162 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
34: They will be treated as separate chains unless you reorder your file.
34: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 4 33
34: 3 'B' 3 25
34: 4 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (33 atoms, 4 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 66 atoms
34: Chain time...
34: Processing chain 3 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 4 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 66 atoms 4 residues
34: Including chain 3 in system: 61 atoms 3 residues
34: Including chain 4 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (292 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 256, now 256
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 652 pairs
34: Before cleaning: 662 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 12 cmap torsion pairs
34: There are 662 dihedrals, 47 impropers, 460 angles
34: 649 pairs, 256 bonds and 0 virtual sites
34: Total mass 1864.131 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34:
34: Merged chains into joint molecule definitions at 1 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (442 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 14 donors and 15 acceptors were found.
34: There are 20 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 173, now 173
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 441 pairs
34: Before cleaning: 446 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 9 cmap torsion pairs
34: There are 446 dihedrals, 29 impropers, 312 angles
34: 438 pairs, 173 bonds and 0 virtual sites
34: Total mass 1262.488 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 255 atoms and 16 residues
34: Total mass in system 1864.131 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 11 86
34: 2 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (86 atoms, 11 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 11 residues with 172 atoms
34: Chain time...
34: Processing chain 2 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 172 atoms 11 residues
34: Including chain 2 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (309 ms)
34: [----------] 8 tests from ChainSep/Pdb2gmxTest (2982 ms total)
34:
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (397 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (228 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (375 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (399 ms)
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest (1400 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 28 tests from 4 test cases ran. (12250 ms total)
34: [ PASSED ] 28 tests.
34/52 Test #34: Pdb2gmx3Test ........................ Passed 12.32 sec
test 35
Start 35: CorrelationsTest
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
35: Test timeout computed to be: 30
35: [==========] Running 11 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 10 tests from AutocorrTest
35: [ RUN ] AutocorrTest.EacNormal
35: [ OK ] AutocorrTest.EacNormal (48 ms)
35: [ RUN ] AutocorrTest.EacNoNormalize
35: [ OK ] AutocorrTest.EacNoNormalize (46 ms)
35: [ RUN ] AutocorrTest.EacCos
35: [ OK ] AutocorrTest.EacCos (29 ms)
35: [ RUN ] AutocorrTest.EacVector
35: [ OK ] AutocorrTest.EacVector (49 ms)
35: [ RUN ] AutocorrTest.EacRcross
35: [ OK ] AutocorrTest.EacRcross (8 ms)
35: [ RUN ] AutocorrTest.EacP0
35: [ OK ] AutocorrTest.EacP0 (41 ms)
35: [ RUN ] AutocorrTest.EacP1
35: [ OK ] AutocorrTest.EacP1 (42 ms)
35: [ RUN ] AutocorrTest.EacP2
35: [ OK ] AutocorrTest.EacP2 (78 ms)
35: [ RUN ] AutocorrTest.EacP3
35: [ OK ] AutocorrTest.EacP3 (30 ms)
35: [ RUN ] AutocorrTest.EacP4
35: [ OK ] AutocorrTest.EacP4 (41 ms)
35: [----------] 10 tests from AutocorrTest (420 ms total)
35:
35: [----------] 1 test from ManyAutocorrelationTest
35: [ RUN ] ManyAutocorrelationTest.Empty
35: [ OK ] ManyAutocorrelationTest.Empty (1 ms)
35: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 11 tests from 2 test cases ran. (448 ms total)
35: [ PASSED ] 11 tests.
35/52 Test #35: CorrelationsTest .................... Passed 0.51 sec
test 36
Start 36: AnalysisDataUnitTests
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 69 tests from 14 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from AnalysisDataInitializationTest
36: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
36: [ OK ] AnalysisDataInitializationTest.BasicInitialization (1 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (1 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
36: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (22 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
36: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms)
36: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/0 (41 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
36: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/1 (26 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
36: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/2 (30 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
36: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/3 (30 ms total)
36:
36: [----------] 4 tests from AnalysisArrayDataTest
36: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
36: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (3 ms)
36: [ RUN ] AnalysisArrayDataTest.StorageWorks
36: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
36: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
36: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
36: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
36:
36: [----------] 6 tests from AverageModuleTest
36: [ RUN ] AverageModuleTest.BasicTest
36: [ OK ] AverageModuleTest.BasicTest (52 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipointData
36: [ OK ] AverageModuleTest.HandlesMultipointData (6 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
36: [ OK ] AverageModuleTest.HandlesMultipleDataSets (7 ms)
36: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
36: [ OK ] AverageModuleTest.HandlesDataSetAveraging (6 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeXAxis
36: [ OK ] AverageModuleTest.CanCustomizeXAxis (5 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
36: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (5 ms)
36: [----------] 6 tests from AverageModuleTest (83 ms total)
36:
36: [----------] 2 tests from FrameAverageModuleTest
36: [ RUN ] FrameAverageModuleTest.BasicTest
36: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
36: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 2 tests from FrameAverageModuleTest (11 ms total)
36:
36: [----------] 7 tests from AnalysisHistogramSettingsTest
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (1 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
36: [----------] 7 tests from AnalysisHistogramSettingsTest (1 ms total)
36:
36: [----------] 2 tests from SimpleHistogramModuleTest
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (13 ms)
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (8 ms)
36: [----------] 2 tests from SimpleHistogramModuleTest (21 ms total)
36:
36: [----------] 3 tests from WeightedHistogramModuleTest
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (8 ms)
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
36: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
36: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (8 ms)
36: [----------] 3 tests from WeightedHistogramModuleTest (26 ms total)
36:
36: [----------] 3 tests from BinAverageModuleTest
36: [ RUN ] BinAverageModuleTest.ComputesCorrectly
36: [ OK ] BinAverageModuleTest.ComputesCorrectly (18 ms)
36: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
36: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (6 ms)
36: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 3 tests from BinAverageModuleTest (32 ms total)
36:
36: [----------] 4 tests from AbstractAverageHistogramTest
36: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
36: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (9 ms)
36: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
36: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (7 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
36: [----------] 4 tests from AbstractAverageHistogramTest (31 ms total)
36:
36: [----------] 3 tests from LifetimeModuleTest
36: [ RUN ] LifetimeModuleTest.BasicTest
36: [ OK ] LifetimeModuleTest.BasicTest (5 ms)
36: [ RUN ] LifetimeModuleTest.CumulativeTest
36: [ OK ] LifetimeModuleTest.CumulativeTest (5 ms)
36: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
36: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 3 tests from LifetimeModuleTest (16 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 69 tests from 14 test cases ran. (364 ms total)
36: [ PASSED ] 69 tests.
36/52 Test #36: AnalysisDataUnitTests ............... Passed 0.44 sec
test 37
Start 37: CoordinateIOTests
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 64 tests from 19 test cases.
37: [----------] Global test environment set-up.
37: [----------] 1 test from OutputSelectorDeathTest
37: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (44 ms)
37: [----------] 1 test from OutputSelectorDeathTest (44 ms total)
37:
37: [----------] 5 tests from TrajectoryFrameWriterTest
37: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (22 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (44 ms)
37: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
37: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (1 ms)
37: [----------] 5 tests from TrajectoryFrameWriterTest (113 ms total)
37:
37: [----------] 5 tests from OutputAdapterContainer
37: [ RUN ] OutputAdapterContainer.MakeEmpty
37: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
37: [ RUN ] OutputAdapterContainer.AddAdapter
37: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectBadAdapter
37: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
37: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
37: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
37: [----------] 5 tests from OutputAdapterContainer (0 ms total)
37:
37: [----------] 5 tests from FlagTest
37: [ RUN ] FlagTest.CanSetSimpleFlag
37: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
37: [ RUN ] FlagTest.CanAddNewBox
37: [ OK ] FlagTest.CanAddNewBox (0 ms)
37: [ RUN ] FlagTest.SetsImplicitPrecisionChange
37: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitStartTimeChange
37: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitTimeStepChange
37: [ OK ] FlagTest.SetsImplicitTimeStepChange (1 ms)
37: [----------] 5 tests from FlagTest (2 ms total)
37:
37: [----------] 5 tests from SetAtomsTest
37: [ RUN ] SetAtomsTest.RemovesExistingAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.RemovesExistingAtoms (22 ms)
37: [ RUN ] SetAtomsTest.AddsNewAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.AddsNewAtoms (22 ms)
37: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (22 ms)
37: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (23 ms)
37: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (22 ms)
37: [----------] 5 tests from SetAtomsTest (111 ms total)
37:
37: [----------] 2 tests from SetBothTimeTest
37: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
37: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
37: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
37: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
37: [----------] 2 tests from SetBothTimeTest (0 ms total)
37:
37: [----------] 2 tests from SetStartTimeTest
37: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
37: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
37: [ RUN ] SetStartTimeTest.WorksWithZeroStart
37: [ OK ] SetStartTimeTest.WorksWithZeroStart (1 ms)
37: [----------] 2 tests from SetStartTimeTest (1 ms total)
37:
37: [----------] 1 test from SetTimeStepTest
37: [ RUN ] SetTimeStepTest.SetTimeStepWorks
37: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
37: [----------] 1 test from SetTimeStepTest (0 ms total)
37:
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (23 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (22 ms)
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (133 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (22 ms)
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (66 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
37:
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (46 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (45 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (46 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (45 ms)
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (182 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (23 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (22 ms)
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (67 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (1 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (22 ms)
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (45 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (1 ms)
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (22 ms)
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (44 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
37:
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (22 ms)
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput (89 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 64 tests from 19 test cases ran. (901 ms total)
37: [ PASSED ] 64 tests.
37/52 Test #37: CoordinateIOTests ................... Passed 0.98 sec
test 38
Start 38: TrajectoryAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 80 tests from 16 test cases.
38: [----------] Global test environment set-up.
38: [----------] 5 tests from ClustsizeTest
38: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 2, cmax: 4, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (49 ms)
38: [ RUN ] ClustsizeTest.NoMolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 1, cmax: 6, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (50 ms)
38: [ RUN ] ClustsizeTest.MolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (76 ms)
38: [ RUN ] ClustsizeTest.MolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 1, cmax: 6, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (15 ms)
38: [ RUN ] ClustsizeTest.MolCSize
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolCSize (15 ms)
38: [----------] 5 tests from ClustsizeTest (205 ms total)
38:
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (6 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (17 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (16 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (41 ms total)
38:
38: [----------] 11 tests from AngleModuleTest
38: [ RUN ] AngleModuleTest.ComputesSimpleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesSimpleAngles (20 ms)
38: [ RUN ] AngleModuleTest.ComputesDihedrals
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesDihedrals (19 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPairAngles (19 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (19 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
38: Reading frames from gro file 'Test system for different angles', 33 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (22 ms)
38: [ RUN ] AngleModuleTest.ComputesMultipleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesMultipleAngles (20 ms)
38: [ RUN ] AngleModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesDynamicSelections (19 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (18 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (20 ms)
38: [----------] 11 tests from AngleModuleTest (219 ms total)
38:
38: [----------] 4 tests from ConvertTrjModuleTest
38: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (64 ms)
38: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (56 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (10 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (11 ms)
38: [----------] 4 tests from ConvertTrjModuleTest (142 ms total)
38:
38: [----------] 3 tests from DistanceModuleTest
38: [ RUN ] DistanceModuleTest.ComputesDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: [ OK ] DistanceModuleTest.ComputesDistances (23 ms)
38: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
38: Number of samples: 4
38: Average distance: 1.81066 nm
38: Standard deviation: 0.79289 nm
38: [ OK ] DistanceModuleTest.ComputesMultipleDistances (25 ms)
38: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2 and res_cog x < 2.8:
38: Number of samples: 3
38: Average distance: 1.72076 nm
38: Standard deviation: 1.24839 nm
38: [ OK ] DistanceModuleTest.HandlesDynamicSelections (24 ms)
38: [----------] 3 tests from DistanceModuleTest (76 ms total)
38:
38: [----------] 2 tests from ExtractClusterModuleTest
38: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
38: trr version: GMX_trn_file (single precision)
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (22 ms)
38: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (16 ms)
38: [----------] 2 tests from ExtractClusterModuleTest (40 ms total)
38:
38: [----------] 2 tests from FreeVolumeModuleTest
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for 40 particles. These were set to zero.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 13
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.02 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
38: Fractional free volume 0.194 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (660 ms)
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 17
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.48 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
38: Fractional free volume 0.200 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (654 ms)
38: [----------] 2 tests from FreeVolumeModuleTest (1315 ms total)
38:
38: [----------] 7 tests from PairDistanceModuleTest
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistances (19 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (19 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (18 ms)
38: [----------] 7 tests from PairDistanceModuleTest (132 ms total)
38:
38: [----------] 5 tests from RdfModuleTest
38: [ RUN ] RdfModuleTest.BasicTest
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.BasicTest (357 ms)
38: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
38: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (104 ms)
38: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (156 ms)
38: [ RUN ] RdfModuleTest.CalculatesSurf
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesSurf (91 ms)
38: [ RUN ] RdfModuleTest.CalculatesXY
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesXY (189 ms)
38: [----------] 5 tests from RdfModuleTest (901 ms total)
38:
38: [----------] 5 tests from SasaModuleTest
38: [ RUN ] SasaModuleTest.BasicTest
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.BasicTest (81 ms)
38: [ RUN ] SasaModuleTest.HandlesSelectedResidues
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesSelectedResidues (49 ms)
38: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (42 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (58 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (85 ms)
38: [----------] 5 tests from SasaModuleTest (327 ms total)
38:
38: [----------] 8 tests from SelectModuleTest
38: [ RUN ] SelectModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.BasicTest (33 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (25 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (25 ms)
38: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (25 ms)
38: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (25 ms)
38: [ RUN ] SelectModuleTest.NormalizesSizes
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.NormalizesSizes (17 ms)
38: [ RUN ] SelectModuleTest.WritesResidueNumbers
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueNumbers (17 ms)
38: [ RUN ] SelectModuleTest.WritesResidueIndices
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueIndices (18 ms)
38: [----------] 8 tests from SelectModuleTest (188 ms total)
38:
38: [----------] 10 tests from SurfaceAreaTest
38: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
38: [ OK ] SurfaceAreaTest.ComputesSinglePoint (1 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
38: [ OK ] SurfaceAreaTest.ComputesTwoPoints (6 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
38: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (6 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints12
38: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints32
38: [ OK ] SurfaceAreaTest.SurfacePoints32 (2 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints42
38: [ OK ] SurfaceAreaTest.SurfacePoints42 (3 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints122
38: [ OK ] SurfaceAreaTest.SurfacePoints122 (7 ms)
38: [ RUN ] SurfaceAreaTest.Computes100Points
38: [ OK ] SurfaceAreaTest.Computes100Points (4 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (14 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (17 ms)
38: [----------] 10 tests from SurfaceAreaTest (63 ms total)
38:
38: [----------] 4 tests from TopologyInformation
38: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
38: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (1 ms)
38: [ RUN ] TopologyInformation.WorksWithGroFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithGroFile (23 ms)
38: [ RUN ] TopologyInformation.WorksWithPdbFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithPdbFile (24 ms)
38: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: For a correct single-point energy evaluation with nsteps = 0, use
38: continuation = yes to avoid constraining the input coordinates.
38:
38: Setting the LD random seed to -1672344272
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
38:
38: NOTE 2 [file lysozyme.top, line 1465]:
38: System has non-zero total charge: 2.000000
38: Total charge should normally be an integer. See
38: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
38: for discussion on how close it should be to an integer.
38:
38:
38:
38: Number of degrees of freedom in T-Coupling group rest is 465.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: NVE simulation with an initial temperature of zero: will use a Verlet
38: buffer of 10%. Check your energy drift!
38:
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
38: Analysing residue names:
38: There are: 10 Protein residues
38: Analysing Protein...
38: This run will generate roughly 0 Mb of data
38: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (3542 ms)
38: [----------] 4 tests from TopologyInformation (3591 ms total)
38:
38: [----------] 4 tests from TrajectoryModuleTest
38: [ RUN ] TrajectoryModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.BasicTest (20 ms)
38: [ RUN ] TrajectoryModuleTest.PlotsXOnly
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.PlotsXOnly (21 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (19 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoForces
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoForces (18 ms)
38: [----------] 4 tests from TrajectoryModuleTest (78 ms total)
38:
38: [----------] 5 tests from UnionFinderTest
38: [ RUN ] UnionFinderTest.WorksEmpty
38: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
38: [ RUN ] UnionFinderTest.BasicMerges
38: [ OK ] UnionFinderTest.BasicMerges (0 ms)
38: [ RUN ] UnionFinderTest.LargerMerges
38: [ OK ] UnionFinderTest.LargerMerges (0 ms)
38: [ RUN ] UnionFinderTest.LongRightMerge
38: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
38: [ RUN ] UnionFinderTest.LongLeftMerge
38: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
38: [----------] 5 tests from UnionFinderTest (1 ms total)
38:
38: [----------] 1 test from MappedUnionFinderTest
38: [ RUN ] MappedUnionFinderTest.BasicMerges
38: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
38: [----------] 1 test from MappedUnionFinderTest (0 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 80 tests from 16 test cases ran. (7322 ms total)
38: [ PASSED ] 80 tests.
38/52 Test #38: TrajectoryAnalysisUnitTests ......... Passed 7.40 sec
test 39
Start 39: EnergyAnalysisUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 7 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 1 test from DhdlTest
39: [ RUN ] DhdlTest.ExtractDhdl
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
39: Note: file tpx version 110, software tpx version 119
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
39:
39:
39: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
39: [ OK ] DhdlTest.ExtractDhdl (96 ms)
39: [----------] 1 test from DhdlTest (99 ms total)
39:
39: [----------] 1 test from OriresTest
39: [ RUN ] OriresTest.ExtractOrires
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
39: Note: file tpx version 111, software tpx version 119
39: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
39: End your selection with 0
39: Selecting all 7 orientation restraints
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
39: [ OK ] OriresTest.ExtractOrires (89 ms)
39: [----------] 1 test from OriresTest (90 ms total)
39:
39: [----------] 3 tests from EnergyTest
39: [ RUN ] EnergyTest.ExtractEnergy
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: [ OK ] EnergyTest.ExtractEnergy (18 ms)
39: [ RUN ] EnergyTest.ExtractEnergyByNumber
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Pres. DC -268.49 3 8.52175 13.2804 (bar)
39: [ OK ] EnergyTest.ExtractEnergyByNumber (15 ms)
39: [ RUN ] EnergyTest.ExtractEnergyMixed
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: [ OK ] EnergyTest.ExtractEnergyMixed (18 ms)
39: [----------] 3 tests from EnergyTest (54 ms total)
39:
39: [----------] 2 tests from ViscosityTest
39: [ RUN ] ViscosityTest.EinsteinViscosity
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosity (47 ms)
39: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosityIntegral (40 ms)
39: [----------] 2 tests from ViscosityTest (91 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 7 tests from 4 test cases ran. (336 ms total)
39: [ PASSED ] 7 tests.
39/52 Test #39: EnergyAnalysisUnitTests ............. Passed 0.40 sec
test 40
Start 40: ToolUnitTests
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 18 tests from 4 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from DumpTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 306325150
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] DumpTest.WorksWithTpr
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
40: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
40: inputrec:
40: integrator = md
40: tinit = 0
40: dt = 0.001
40: nsteps = 0
40: init-step = 0
40: simulation-part = 1
40: comm-mode = Linear
40: nstcomm = 100
40: bd-fric = 0
40: ld-seed = 306325150
40: emtol = 10
40: emstep = 0.01
40: niter = 20
40: fcstep = 0
40: nstcgsteep = 1000
40: nbfgscorr = 10
40: rtpi = 0.05
40: nstxout = 0
40: nstvout = 0
40: nstfout = 0
40: nstlog = 1000
40: nstcalcenergy = 100
40: nstenergy = 1000
40: nstxout-compressed = 0
40: compressed-x-precision = 1000
40: cutoff-scheme = Verlet
40: nstlist = 10
40: pbc = xyz
40: periodic-molecules = false
40: verlet-buffer-tolerance = -1
40: rlist = 1.1
40: coulombtype = Cut-off
40: coulomb-modifier = Potential-shift
40: rcoulomb-switch = 0
40: rcoulomb = 1
40: epsilon-r = 1
40: epsilon-rf = inf
40: vdw-type = Cut-off
40: vdw-modifier = Potential-shift
40: rvdw-switch = 0
40: rvdw = 1
40: DispCorr = No
40: table-extension = 1
40: fourierspacing = 0.12
40: fourier-nx = 0
40: fourier-ny = 0
40: fourier-nz = 0
40: pme-order = 4
40: ewald-rtol = 1e-05
40: ewald-rtol-lj = 0.001
40: lj-pme-comb-rule = Geometric
40: ewald-geometry = 0
40: epsilon-surface = 0
40: tcoupl = No
40: nsttcouple = -1
40: nh-chain-length = 0
40: print-nose-hoover-chain-variables = false
40: pcoupl = No
40: pcoupltype = Isotropic
40: nstpcouple = -1
40: tau-p = 1
40: compressibility (3x3):
40: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p (3x3):
40: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: refcoord-scaling = No
40: posres-com (3):
40: posres-com[0]= 0.00000e+00
40: posres-com[1]= 0.00000e+00
40: posres-com[2]= 0.00000e+00
40: posres-comB (3):
40: posres-comB[0]= 0.00000e+00
40: posres-comB[1]= 0.00000e+00
40: posres-comB[2]= 0.00000e+00
40: QMMM = false
40: QMconstraints = 0
40: QMMMscheme = 0
40: MMChargeScaleFactor = 1
40: qm-opts:
40: ngQM = 0
40: constraint-algorithm = Lincs
40: continuation = false
40: Shake-SOR = false
40: shake-tol = 0.0001
40: lincs-order = 4
40: lincs-iter = 1
40: lincs-warnangle = 30
40: nwall = 0
40: wall-type = 9-3
40: wall-r-linpot = -1
40: wall-atomtype[0] = -1
40: wall-atomtype[1] = -1
40: wall-density[0] = 0
40: wall-density[1] = 0
40: wall-ewald-zfac = 3
40: pull = false
40: awh = false
40: rotation = false
40: interactiveMD = false
40: disre = No
40: disre-weighting = Conservative
40: disre-mixed = false
40: dr-fc = 1000
40: dr-tau = 0
40: nstdisreout = 100
40: orire-fc = 0
40: orire-tau = 0
40: nstorireout = 100
40: free-energy = no
40: cos-acceleration = 0
40: deform (3x3):
40: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: simulated-tempering = false
40: swapcoords = no
40: userint1 = 0
40: userint2 = 0
40: userint3 = 0
40: userint4 = 0
40: userreal1 = 0
40: userreal2 = 0
40: userreal3 = 0
40: userreal4 = 0
40: applied-forces:
40: electric-field:
40: x:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: y:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: z:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: density-guided-simulation:
40: active = false
40: group = protein
40: similarity-measure = inner-product
40: atom-spreading-weight = unity
40: force-constant = 1e+09
40: gaussian-transform-spreading-width = 0.2
40: gaussian-transform-spreading-range-in-multiples-of-width = 4
40: reference-density-filename = reference.mrc
40: nst = 1
40: normalize-densities = true
40: adaptive-force-scaling = false
40: adaptive-force-scaling-time-constant = 4
40: grpopts:
40: nrdf: 465
40: ref-t: 0
40: tau-t: 0
40: annealing: No
40: annealing-npoints: 0
40: acc: 0 0 0
40: nfreeze: N N N
40: energygrp-flags[ 0]: 0
40: header:
40: bIr = present
40: bBox = present
40: bTop = present
40: bX = present
40: bV = present
40: bF = not present
40: natoms = 156
40: lambda = 0.000000e+00
40: buffer size = 59422
40: topology:
40: name="First 10 residues from 1AKI"
40: #atoms = 156
40: #molblock = 1
40: molblock (0):
40: moltype = 0 "Protein_chain_B"
40: #molecules = 1
40: #posres_xA = 0
40: #posres_xB = 0
40: bIntermolecularInteractions = false
40: ffparams:
40: atnr=10
40: ntypes=212
40: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
40: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
40: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
40: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
40: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
40: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
40: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
40: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
40: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
40: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
40: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06
40: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
40: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
40: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
40: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
40: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
40: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
40: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
40: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
40: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
40: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08
40: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
40: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
40: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
40: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
40: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
40: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
40: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
40: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
40: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
40: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05
40: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
40: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
40: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
40: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
40: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
40: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
40: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
40: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
40: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
40: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
40: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
40: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
40: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
40: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
40: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
40: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
40: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
40: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
40: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
40: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
40: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
40: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
40: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
40: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
40: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
40: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
40: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
40: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
40: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
40: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
40: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
40: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
40: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
40: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
40: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
40: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
40: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
40: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
40: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
40: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
40: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
40: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
40: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
40: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
40: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
40: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
40: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
40: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
40: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
40: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
40: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
40: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
40: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
40: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
40: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
40: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
40: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
40: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
40: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
40: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
40: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
40: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
40: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
40: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
40: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
40: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
40: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
40: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
40: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
40: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
40: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
40: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
40: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
40: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
40: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
40: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
40: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
40: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
40: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
40: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
40: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
40: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
40: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
40: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
40: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
40: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
40: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
40: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
40: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
40: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
40: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
40: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
40: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
40: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
40: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
40: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
40: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
40: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
40: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
40: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
40: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
40: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
40: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
40: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
40: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
40: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
40: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
40: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
40: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
40: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
40: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
40: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
40: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
40: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
40: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
40: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
40: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
40: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
40: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
40: reppow = 12
40: fudgeQQ = 0.5
40: cmap
40: atomtypes:
40: atomtype[ 0]={atomnumber= 7}
40: atomtype[ 1]={atomnumber= 1}
40: atomtype[ 2]={atomnumber= 6}
40: atomtype[ 3]={atomnumber= 1}
40: atomtype[ 4]={atomnumber= 6}
40: atomtype[ 5]={atomnumber= 8}
40: atomtype[ 6]={atomnumber= 6}
40: atomtype[ 7]={atomnumber= 1}
40: atomtype[ 8]={atomnumber= 6}
40: atomtype[ 9]={atomnumber= 16}
40: moltype (0):
40: name="Protein_chain_B"
40: atoms:
40: atom (156):
40: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
40: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
40: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
40: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
40: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
40: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
40: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
40: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
40: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
40: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
40: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
40: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
40: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
40: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
40: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
40: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
40: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
40: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
40: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
40: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
40: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
40: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
40: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
40: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
40: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
40: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
40: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
40: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
40: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
40: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
40: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
40: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
40: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
40: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
40: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
40: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
40: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
40: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
40: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
40: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
40: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
40: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
40: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
40: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
40: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
40: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
40: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
40: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
40: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
40: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
40: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
40: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
40: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
40: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
40: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
40: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
40: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
40: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
40: atom (156):
40: atom[0]={name="N"}
40: atom[1]={name="H1"}
40: atom[2]={name="H2"}
40: atom[3]={name="H3"}
40: atom[4]={name="CA"}
40: atom[5]={name="HA"}
40: atom[6]={name="CB"}
40: atom[7]={name="HB1"}
40: atom[8]={name="HB2"}
40: atom[9]={name="CG"}
40: atom[10]={name="HG1"}
40: atom[11]={name="HG2"}
40: atom[12]={name="CD"}
40: atom[13]={name="HD1"}
40: atom[14]={name="HD2"}
40: atom[15]={name="CE"}
40: atom[16]={name="HE1"}
40: atom[17]={name="HE2"}
40: atom[18]={name="NZ"}
40: atom[19]={name="HZ1"}
40: atom[20]={name="HZ2"}
40: atom[21]={name="HZ3"}
40: atom[22]={name="C"}
40: atom[23]={name="O"}
40: atom[24]={name="N"}
40: atom[25]={name="H"}
40: atom[26]={name="CA"}
40: atom[27]={name="HA"}
40: atom[28]={name="CB"}
40: atom[29]={name="HB"}
40: atom[30]={name="CG1"}
40: atom[31]={name="HG11"}
40: atom[32]={name="HG12"}
40: atom[33]={name="HG13"}
40: atom[34]={name="CG2"}
40: atom[35]={name="HG21"}
40: atom[36]={name="HG22"}
40: atom[37]={name="HG23"}
40: atom[38]={name="C"}
40: atom[39]={name="O"}
40: atom[40]={name="N"}
40: atom[41]={name="H"}
40: atom[42]={name="CA"}
40: atom[43]={name="HA"}
40: atom[44]={name="CB"}
40: atom[45]={name="HB1"}
40: atom[46]={name="HB2"}
40: atom[47]={name="CG"}
40: atom[48]={name="CD1"}
40: atom[49]={name="HD1"}
40: atom[50]={name="CD2"}
40: atom[51]={name="HD2"}
40: atom[52]={name="CE1"}
40: atom[53]={name="HE1"}
40: atom[54]={name="CE2"}
40: atom[55]={name="HE2"}
40: atom[56]={name="CZ"}
40: atom[57]={name="HZ"}
40: atom[58]={name="C"}
40: atom[59]={name="O"}
40: atom[60]={name="N"}
40: atom[61]={name="H"}
40: atom[62]={name="CA"}
40: atom[63]={name="HA1"}
40: atom[64]={name="HA2"}
40: atom[65]={name="C"}
40: atom[66]={name="O"}
40: atom[67]={name="N"}
40: atom[68]={name="H"}
40: atom[69]={name="CA"}
40: atom[70]={name="HA"}
40: atom[71]={name="CB"}
40: atom[72]={name="HB1"}
40: atom[73]={name="HB2"}
40: atom[74]={name="CG"}
40: atom[75]={name="HG1"}
40: atom[76]={name="HG2"}
40: atom[77]={name="CD"}
40: atom[78]={name="HD1"}
40: atom[79]={name="HD2"}
40: atom[80]={name="NE"}
40: atom[81]={name="HE"}
40: atom[82]={name="CZ"}
40: atom[83]={name="NH1"}
40: atom[84]={name="HH11"}
40: atom[85]={name="HH12"}
40: atom[86]={name="NH2"}
40: atom[87]={name="HH21"}
40: atom[88]={name="HH22"}
40: atom[89]={name="C"}
40: atom[90]={name="O"}
40: atom[91]={name="N"}
40: atom[92]={name="H"}
40: atom[93]={name="CA"}
40: atom[94]={name="HA"}
40: atom[95]={name="CB"}
40: atom[96]={name="HB1"}
40: atom[97]={name="HB2"}
40: atom[98]={name="SG"}
40: atom[99]={name="HG"}
40: atom[100]={name="C"}
40: atom[101]={name="O"}
40: atom[102]={name="N"}
40: atom[103]={name="H"}
40: atom[104]={name="CA"}
40: atom[105]={name="HA"}
40: atom[106]={name="CB"}
40: atom[107]={name="HB1"}
40: atom[108]={name="HB2"}
40: atom[109]={name="CG"}
40: atom[110]={name="HG1"}
40: atom[111]={name="HG2"}
40: atom[112]={name="CD"}
40: atom[113]={name="OE1"}
40: atom[114]={name="OE2"}
40: atom[115]={name="C"}
40: atom[116]={name="O"}
40: atom[117]={name="N"}
40: atom[118]={name="H"}
40: atom[119]={name="CA"}
40: atom[120]={name="HA"}
40: atom[121]={name="CB"}
40: atom[122]={name="HB1"}
40: atom[123]={name="HB2"}
40: atom[124]={name="CG"}
40: atom[125]={name="HG"}
40: atom[126]={name="CD1"}
40: atom[127]={name="HD11"}
40: atom[128]={name="HD12"}
40: atom[129]={name="HD13"}
40: atom[130]={name="CD2"}
40: atom[131]={name="HD21"}
40: atom[132]={name="HD22"}
40: atom[133]={name="HD23"}
40: atom[134]={name="C"}
40: atom[135]={name="O"}
40: atom[136]={name="N"}
40: atom[137]={name="H"}
40: atom[138]={name="CA"}
40: atom[139]={name="HA"}
40: atom[140]={name="CB"}
40: atom[141]={name="HB1"}
40: atom[142]={name="HB2"}
40: atom[143]={name="HB3"}
40: atom[144]={name="C"}
40: atom[145]={name="O"}
40: atom[146]={name="N"}
40: atom[147]={name="H"}
40: atom[148]={name="CA"}
40: atom[149]={name="HA"}
40: atom[150]={name="CB"}
40: atom[151]={name="HB1"}
40: atom[152]={name="HB2"}
40: atom[153]={name="HB3"}
40: atom[154]={name="C"}
40: atom[155]={name="O"}
40: type (156):
40: type[0]={name="opls_287",nameB="opls_287"}
40: type[1]={name="opls_290",nameB="opls_290"}
40: type[2]={name="opls_290",nameB="opls_290"}
40: type[3]={name="opls_290",nameB="opls_290"}
40: type[4]={name="opls_293B",nameB="opls_293B"}
40: type[5]={name="opls_140",nameB="opls_140"}
40: type[6]={name="opls_136",nameB="opls_136"}
40: type[7]={name="opls_140",nameB="opls_140"}
40: type[8]={name="opls_140",nameB="opls_140"}
40: type[9]={name="opls_136",nameB="opls_136"}
40: type[10]={name="opls_140",nameB="opls_140"}
40: type[11]={name="opls_140",nameB="opls_140"}
40: type[12]={name="opls_136",nameB="opls_136"}
40: type[13]={name="opls_140",nameB="opls_140"}
40: type[14]={name="opls_140",nameB="opls_140"}
40: type[15]={name="opls_292",nameB="opls_292"}
40: type[16]={name="opls_140",nameB="opls_140"}
40: type[17]={name="opls_140",nameB="opls_140"}
40: type[18]={name="opls_287",nameB="opls_287"}
40: type[19]={name="opls_290",nameB="opls_290"}
40: type[20]={name="opls_290",nameB="opls_290"}
40: type[21]={name="opls_290",nameB="opls_290"}
40: type[22]={name="opls_235",nameB="opls_235"}
40: type[23]={name="opls_236",nameB="opls_236"}
40: type[24]={name="opls_238",nameB="opls_238"}
40: type[25]={name="opls_241",nameB="opls_241"}
40: type[26]={name="opls_224B",nameB="opls_224B"}
40: type[27]={name="opls_140",nameB="opls_140"}
40: type[28]={name="opls_137",nameB="opls_137"}
40: type[29]={name="opls_140",nameB="opls_140"}
40: type[30]={name="opls_135",nameB="opls_135"}
40: type[31]={name="opls_140",nameB="opls_140"}
40: type[32]={name="opls_140",nameB="opls_140"}
40: type[33]={name="opls_140",nameB="opls_140"}
40: type[34]={name="opls_135",nameB="opls_135"}
40: type[35]={name="opls_140",nameB="opls_140"}
40: type[36]={name="opls_140",nameB="opls_140"}
40: type[37]={name="opls_140",nameB="opls_140"}
40: type[38]={name="opls_235",nameB="opls_235"}
40: type[39]={name="opls_236",nameB="opls_236"}
40: type[40]={name="opls_238",nameB="opls_238"}
40: type[41]={name="opls_241",nameB="opls_241"}
40: type[42]={name="opls_224B",nameB="opls_224B"}
40: type[43]={name="opls_140",nameB="opls_140"}
40: type[44]={name="opls_149",nameB="opls_149"}
40: type[45]={name="opls_140",nameB="opls_140"}
40: type[46]={name="opls_140",nameB="opls_140"}
40: type[47]={name="opls_145",nameB="opls_145"}
40: type[48]={name="opls_145",nameB="opls_145"}
40: type[49]={name="opls_146",nameB="opls_146"}
40: type[50]={name="opls_145",nameB="opls_145"}
40: type[51]={name="opls_146",nameB="opls_146"}
40: type[52]={name="opls_145",nameB="opls_145"}
40: type[53]={name="opls_146",nameB="opls_146"}
40: type[54]={name="opls_145",nameB="opls_145"}
40: type[55]={name="opls_146",nameB="opls_146"}
40: type[56]={name="opls_145",nameB="opls_145"}
40: type[57]={name="opls_146",nameB="opls_146"}
40: type[58]={name="opls_235",nameB="opls_235"}
40: type[59]={name="opls_236",nameB="opls_236"}
40: type[60]={name="opls_238",nameB="opls_238"}
40: type[61]={name="opls_241",nameB="opls_241"}
40: type[62]={name="opls_223B",nameB="opls_223B"}
40: type[63]={name="opls_140",nameB="opls_140"}
40: type[64]={name="opls_140",nameB="opls_140"}
40: type[65]={name="opls_235",nameB="opls_235"}
40: type[66]={name="opls_236",nameB="opls_236"}
40: type[67]={name="opls_238",nameB="opls_238"}
40: type[68]={name="opls_241",nameB="opls_241"}
40: type[69]={name="opls_224B",nameB="opls_224B"}
40: type[70]={name="opls_140",nameB="opls_140"}
40: type[71]={name="opls_136",nameB="opls_136"}
40: type[72]={name="opls_140",nameB="opls_140"}
40: type[73]={name="opls_140",nameB="opls_140"}
40: type[74]={name="opls_308",nameB="opls_308"}
40: type[75]={name="opls_140",nameB="opls_140"}
40: type[76]={name="opls_140",nameB="opls_140"}
40: type[77]={name="opls_307",nameB="opls_307"}
40: type[78]={name="opls_140",nameB="opls_140"}
40: type[79]={name="opls_140",nameB="opls_140"}
40: type[80]={name="opls_303",nameB="opls_303"}
40: type[81]={name="opls_304",nameB="opls_304"}
40: type[82]={name="opls_302",nameB="opls_302"}
40: type[83]={name="opls_300",nameB="opls_300"}
40: type[84]={name="opls_301",nameB="opls_301"}
40: type[85]={name="opls_301",nameB="opls_301"}
40: type[86]={name="opls_300",nameB="opls_300"}
40: type[87]={name="opls_301",nameB="opls_301"}
40: type[88]={name="opls_301",nameB="opls_301"}
40: type[89]={name="opls_235",nameB="opls_235"}
40: type[90]={name="opls_236",nameB="opls_236"}
40: type[91]={name="opls_238",nameB="opls_238"}
40: type[92]={name="opls_241",nameB="opls_241"}
40: type[93]={name="opls_224B",nameB="opls_224B"}
40: type[94]={name="opls_140",nameB="opls_140"}
40: type[95]={name="opls_206",nameB="opls_206"}
40: type[96]={name="opls_140",nameB="opls_140"}
40: type[97]={name="opls_140",nameB="opls_140"}
40: type[98]={name="opls_200",nameB="opls_200"}
40: type[99]={name="opls_204",nameB="opls_204"}
40: type[100]={name="opls_235",nameB="opls_235"}
40: type[101]={name="opls_236",nameB="opls_236"}
40: type[102]={name="opls_238",nameB="opls_238"}
40: type[103]={name="opls_241",nameB="opls_241"}
40: type[104]={name="opls_224B",nameB="opls_224B"}
40: type[105]={name="opls_140",nameB="opls_140"}
40: type[106]={name="opls_136",nameB="opls_136"}
40: type[107]={name="opls_140",nameB="opls_140"}
40: type[108]={name="opls_140",nameB="opls_140"}
40: type[109]={name="opls_274",nameB="opls_274"}
40: type[110]={name="opls_140",nameB="opls_140"}
40: type[111]={name="opls_140",nameB="opls_140"}
40: type[112]={name="opls_271",nameB="opls_271"}
40: type[113]={name="opls_272",nameB="opls_272"}
40: type[114]={name="opls_272",nameB="opls_272"}
40: type[115]={name="opls_235",nameB="opls_235"}
40: type[116]={name="opls_236",nameB="opls_236"}
40: type[117]={name="opls_238",nameB="opls_238"}
40: type[118]={name="opls_241",nameB="opls_241"}
40: type[119]={name="opls_224B",nameB="opls_224B"}
40: type[120]={name="opls_140",nameB="opls_140"}
40: type[121]={name="opls_136",nameB="opls_136"}
40: type[122]={name="opls_140",nameB="opls_140"}
40: type[123]={name="opls_140",nameB="opls_140"}
40: type[124]={name="opls_137",nameB="opls_137"}
40: type[125]={name="opls_140",nameB="opls_140"}
40: type[126]={name="opls_135",nameB="opls_135"}
40: type[127]={name="opls_140",nameB="opls_140"}
40: type[128]={name="opls_140",nameB="opls_140"}
40: type[129]={name="opls_140",nameB="opls_140"}
40: type[130]={name="opls_135",nameB="opls_135"}
40: type[131]={name="opls_140",nameB="opls_140"}
40: type[132]={name="opls_140",nameB="opls_140"}
40: type[133]={name="opls_140",nameB="opls_140"}
40: type[134]={name="opls_235",nameB="opls_235"}
40: type[135]={name="opls_236",nameB="opls_236"}
40: type[136]={name="opls_238",nameB="opls_238"}
40: type[137]={name="opls_241",nameB="opls_241"}
40: type[138]={name="opls_224B",nameB="opls_224B"}
40: type[139]={name="opls_140",nameB="opls_140"}
40: type[140]={name="opls_135",nameB="opls_135"}
40: type[141]={name="opls_140",nameB="opls_140"}
40: type[142]={name="opls_140",nameB="opls_140"}
40: type[143]={name="opls_140",nameB="opls_140"}
40: type[144]={name="opls_235",nameB="opls_235"}
40: type[145]={name="opls_236",nameB="opls_236"}
40: type[146]={name="opls_238",nameB="opls_238"}
40: type[147]={name="opls_241",nameB="opls_241"}
40: type[148]={name="opls_224B",nameB="opls_224B"}
40: type[149]={name="opls_140",nameB="opls_140"}
40: type[150]={name="opls_135",nameB="opls_135"}
40: type[151]={name="opls_140",nameB="opls_140"}
40: type[152]={name="opls_140",nameB="opls_140"}
40: type[153]={name="opls_140",nameB="opls_140"}
40: type[154]={name="opls_235",nameB="opls_235"}
40: type[155]={name="opls_236",nameB="opls_236"}
40: residue (10):
40: residue[0]={name="LYS", nr=1, ic=' '}
40: residue[1]={name="VAL", nr=2, ic=' '}
40: residue[2]={name="PHE", nr=3, ic=' '}
40: residue[3]={name="GLY", nr=4, ic=' '}
40: residue[4]={name="ARG", nr=5, ic=' '}
40: residue[5]={name="CYS", nr=6, ic=' '}
40: residue[6]={name="GLU", nr=7, ic=' '}
40: residue[7]={name="LEU", nr=8, ic=' '}
40: residue[8]={name="ALA", nr=9, ic=' '}
40: residue[9]={name="ALA", nr=10, ic=' '}
40: excls:
40: nr=156
40: nra=1828
40: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
40: 23, 24, 25, 26}
40: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
40: 14, 15, 22, 23, 24}
40: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
40: 16, 17, 18, 22}
40: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
40: 17, 18, 19, 20, 21}
40: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
40: 19, 20, 21}
40: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
40: 25, 26, 27, 28, 38}
40: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
40: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
40: 30, 34, 38, 39, 40}
40: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
40: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
40: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
40: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40}
40: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
40: 34, 35, 36, 37, 38, 39, 40}
40: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40, 41, 42, 43, 44, 58}
40: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
40: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
40: 45, 46, 47, 58, 59, 60}
40: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
40: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
40: 48, 50, 58, 59, 60, 61, 62}
40: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60}
40: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
40: 50, 51, 52, 54, 58, 59, 60}
40: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
40: 52, 53, 54, 55, 56, 58}
40: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
40: 54, 56, 57}
40: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
40: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
40: 55, 56, 57}
40: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
40: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
40: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
40: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
40: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
40: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60, 61, 62, 63, 64, 65}
40: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
40: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
40: 65, 66, 67}
40: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
40: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
40: 68, 69}
40: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
40: 70, 71, 89}
40: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
40: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
40: 72, 73, 74, 89, 90, 91}
40: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
40: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
40: 75, 76, 77, 89, 90, 91, 92, 93}
40: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
40: 91}
40: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
40: 77, 78, 79, 80, 89, 90, 91}
40: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
40: 79, 80, 81, 82, 89}
40: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
40: 81, 82, 83, 86}
40: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
40: 84, 85, 86, 87, 88}
40: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
40: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
40: 86, 87, 88}
40: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
40: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
40: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
40: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
40: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
40: 90, 91, 92, 93, 94, 95, 100}
40: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
40: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
40: 95, 96, 97, 98, 100, 101, 102}
40: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
40: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
40: 98, 99, 100, 101, 102, 103, 104}
40: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102}
40: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
40: 100, 101, 102}
40: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
40: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102, 103, 104, 105, 106, 115}
40: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
40: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
40: 105, 106, 107, 108, 109, 115, 116, 117}
40: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
40: 115}
40: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
40: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
40: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117}
40: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 110, 111, 112, 113, 114, 115, 116, 117}
40: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 113, 114, 115}
40: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
40: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
40: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117, 118, 119, 120, 121, 134}
40: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119}
40: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119, 120, 121, 122, 123, 124, 134, 135, 136}
40: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
40: 134}
40: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
40: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
40: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136}
40: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
40: 136}
40: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 127, 128, 129, 130, 131, 132, 133, 134}
40: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136, 137, 138, 139, 140, 144}
40: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138}
40: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138, 139, 140, 141, 142, 143, 144, 145, 146}
40: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
40: 144}
40: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
40: 141, 142, 143, 144, 145, 146, 147, 148}
40: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146, 147, 148, 149, 150, 154}
40: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148}
40: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148, 149, 150, 151, 152, 153, 154, 155}
40: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
40: 154}
40: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
40: 151, 152, 153, 154, 155}
40: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
40: Bond:
40: nr: 468
40: iatoms:
40: 0 type=100 (BONDS) 0 1
40: 1 type=100 (BONDS) 0 2
40: 2 type=100 (BONDS) 0 3
40: 3 type=101 (BONDS) 0 4
40: 4 type=102 (BONDS) 4 5
40: 5 type=103 (BONDS) 4 6
40: 6 type=104 (BONDS) 4 22
40: 7 type=102 (BONDS) 6 7
40: 8 type=102 (BONDS) 6 8
40: 9 type=103 (BONDS) 6 9
40: 10 type=102 (BONDS) 9 10
40: 11 type=102 (BONDS) 9 11
40: 12 type=103 (BONDS) 9 12
40: 13 type=102 (BONDS) 12 13
40: 14 type=102 (BONDS) 12 14
40: 15 type=103 (BONDS) 12 15
40: 16 type=102 (BONDS) 15 16
40: 17 type=102 (BONDS) 15 17
40: 18 type=101 (BONDS) 15 18
40: 19 type=100 (BONDS) 18 19
40: 20 type=100 (BONDS) 18 20
40: 21 type=100 (BONDS) 18 21
40: 22 type=105 (BONDS) 22 23
40: 23 type=106 (BONDS) 22 24
40: 24 type=100 (BONDS) 24 25
40: 25 type=107 (BONDS) 24 26
40: 26 type=102 (BONDS) 26 27
40: 27 type=103 (BONDS) 26 28
40: 28 type=104 (BONDS) 26 38
40: 29 type=102 (BONDS) 28 29
40: 30 type=103 (BONDS) 28 30
40: 31 type=103 (BONDS) 28 34
40: 32 type=102 (BONDS) 30 31
40: 33 type=102 (BONDS) 30 32
40: 34 type=102 (BONDS) 30 33
40: 35 type=102 (BONDS) 34 35
40: 36 type=102 (BONDS) 34 36
40: 37 type=102 (BONDS) 34 37
40: 38 type=105 (BONDS) 38 39
40: 39 type=106 (BONDS) 38 40
40: 40 type=100 (BONDS) 40 41
40: 41 type=107 (BONDS) 40 42
40: 42 type=102 (BONDS) 42 43
40: 43 type=103 (BONDS) 42 44
40: 44 type=104 (BONDS) 42 58
40: 45 type=102 (BONDS) 44 45
40: 46 type=102 (BONDS) 44 46
40: 47 type=108 (BONDS) 44 47
40: 48 type=109 (BONDS) 47 48
40: 49 type=109 (BONDS) 47 50
40: 50 type=110 (BONDS) 48 49
40: 51 type=109 (BONDS) 48 52
40: 52 type=110 (BONDS) 50 51
40: 53 type=109 (BONDS) 50 54
40: 54 type=110 (BONDS) 52 53
40: 55 type=109 (BONDS) 52 56
40: 56 type=110 (BONDS) 54 55
40: 57 type=109 (BONDS) 54 56
40: 58 type=110 (BONDS) 56 57
40: 59 type=105 (BONDS) 58 59
40: 60 type=106 (BONDS) 58 60
40: 61 type=100 (BONDS) 60 61
40: 62 type=107 (BONDS) 60 62
40: 63 type=102 (BONDS) 62 63
40: 64 type=102 (BONDS) 62 64
40: 65 type=104 (BONDS) 62 65
40: 66 type=105 (BONDS) 65 66
40: 67 type=106 (BONDS) 65 67
40: 68 type=100 (BONDS) 67 68
40: 69 type=107 (BONDS) 67 69
40: 70 type=102 (BONDS) 69 70
40: 71 type=103 (BONDS) 69 71
40: 72 type=104 (BONDS) 69 89
40: 73 type=102 (BONDS) 71 72
40: 74 type=102 (BONDS) 71 73
40: 75 type=103 (BONDS) 71 74
40: 76 type=102 (BONDS) 74 75
40: 77 type=102 (BONDS) 74 76
40: 78 type=103 (BONDS) 74 77
40: 79 type=102 (BONDS) 77 78
40: 80 type=102 (BONDS) 77 79
40: 81 type=111 (BONDS) 77 80
40: 82 type=100 (BONDS) 80 81
40: 83 type=112 (BONDS) 80 82
40: 84 type=112 (BONDS) 82 83
40: 85 type=112 (BONDS) 82 86
40: 86 type=100 (BONDS) 83 84
40: 87 type=100 (BONDS) 83 85
40: 88 type=100 (BONDS) 86 87
40: 89 type=100 (BONDS) 86 88
40: 90 type=105 (BONDS) 89 90
40: 91 type=106 (BONDS) 89 91
40: 92 type=100 (BONDS) 91 92
40: 93 type=107 (BONDS) 91 93
40: 94 type=102 (BONDS) 93 94
40: 95 type=103 (BONDS) 93 95
40: 96 type=104 (BONDS) 93 100
40: 97 type=102 (BONDS) 95 96
40: 98 type=102 (BONDS) 95 97
40: 99 type=113 (BONDS) 95 98
40: 100 type=114 (BONDS) 98 99
40: 101 type=105 (BONDS) 100 101
40: 102 type=106 (BONDS) 100 102
40: 103 type=100 (BONDS) 102 103
40: 104 type=107 (BONDS) 102 104
40: 105 type=102 (BONDS) 104 105
40: 106 type=103 (BONDS) 104 106
40: 107 type=104 (BONDS) 104 115
40: 108 type=102 (BONDS) 106 107
40: 109 type=102 (BONDS) 106 108
40: 110 type=103 (BONDS) 106 109
40: 111 type=102 (BONDS) 109 110
40: 112 type=102 (BONDS) 109 111
40: 113 type=104 (BONDS) 109 112
40: 114 type=115 (BONDS) 112 113
40: 115 type=115 (BONDS) 112 114
40: 116 type=105 (BONDS) 115 116
40: 117 type=106 (BONDS) 115 117
40: 118 type=100 (BONDS) 117 118
40: 119 type=107 (BONDS) 117 119
40: 120 type=102 (BONDS) 119 120
40: 121 type=103 (BONDS) 119 121
40: 122 type=104 (BONDS) 119 134
40: 123 type=102 (BONDS) 121 122
40: 124 type=102 (BONDS) 121 123
40: 125 type=103 (BONDS) 121 124
40: 126 type=102 (BONDS) 124 125
40: 127 type=103 (BONDS) 124 126
40: 128 type=103 (BONDS) 124 130
40: 129 type=102 (BONDS) 126 127
40: 130 type=102 (BONDS) 126 128
40: 131 type=102 (BONDS) 126 129
40: 132 type=102 (BONDS) 130 131
40: 133 type=102 (BONDS) 130 132
40: 134 type=102 (BONDS) 130 133
40: 135 type=105 (BONDS) 134 135
40: 136 type=106 (BONDS) 134 136
40: 137 type=100 (BONDS) 136 137
40: 138 type=107 (BONDS) 136 138
40: 139 type=102 (BONDS) 138 139
40: 140 type=103 (BONDS) 138 140
40: 141 type=104 (BONDS) 138 144
40: 142 type=102 (BONDS) 140 141
40: 143 type=102 (BONDS) 140 142
40: 144 type=102 (BONDS) 140 143
40: 145 type=105 (BONDS) 144 145
40: 146 type=106 (BONDS) 144 146
40: 147 type=100 (BONDS) 146 147
40: 148 type=107 (BONDS) 146 148
40: 149 type=102 (BONDS) 148 149
40: 150 type=103 (BONDS) 148 150
40: 151 type=104 (BONDS) 148 154
40: 152 type=102 (BONDS) 150 151
40: 153 type=102 (BONDS) 150 152
40: 154 type=102 (BONDS) 150 153
40: 155 type=105 (BONDS) 154 155
40: G96Bond:
40: nr: 0
40: Morse:
40: nr: 0
40: Cubic Bonds:
40: nr: 0
40: Connect Bonds:
40: nr: 0
40: Harmonic Pot.:
40: nr: 0
40: FENE Bonds:
40: nr: 0
40: Tab. Bonds:
40: nr: 0
40: Tab. Bonds NC:
40: nr: 0
40: Restraint Pot.:
40: nr: 0
40: Angle:
40: nr: 1124
40: iatoms:
40: 0 type=116 (ANGLES) 1 0 2
40: 1 type=116 (ANGLES) 1 0 3
40: 2 type=116 (ANGLES) 1 0 4
40: 3 type=116 (ANGLES) 2 0 3
40: 4 type=116 (ANGLES) 2 0 4
40: 5 type=116 (ANGLES) 3 0 4
40: 6 type=116 (ANGLES) 0 4 5
40: 7 type=117 (ANGLES) 0 4 6
40: 8 type=117 (ANGLES) 0 4 22
40: 9 type=118 (ANGLES) 5 4 6
40: 10 type=116 (ANGLES) 5 4 22
40: 11 type=119 (ANGLES) 6 4 22
40: 12 type=118 (ANGLES) 4 6 7
40: 13 type=118 (ANGLES) 4 6 8
40: 14 type=120 (ANGLES) 4 6 9
40: 15 type=121 (ANGLES) 7 6 8
40: 16 type=118 (ANGLES) 7 6 9
40: 17 type=118 (ANGLES) 8 6 9
40: 18 type=118 (ANGLES) 6 9 10
40: 19 type=118 (ANGLES) 6 9 11
40: 20 type=120 (ANGLES) 6 9 12
40: 21 type=121 (ANGLES) 10 9 11
40: 22 type=118 (ANGLES) 10 9 12
40: 23 type=118 (ANGLES) 11 9 12
40: 24 type=118 (ANGLES) 9 12 13
40: 25 type=118 (ANGLES) 9 12 14
40: 26 type=120 (ANGLES) 9 12 15
40: 27 type=121 (ANGLES) 13 12 14
40: 28 type=118 (ANGLES) 13 12 15
40: 29 type=118 (ANGLES) 14 12 15
40: 30 type=118 (ANGLES) 12 15 16
40: 31 type=118 (ANGLES) 12 15 17
40: 32 type=117 (ANGLES) 12 15 18
40: 33 type=121 (ANGLES) 16 15 17
40: 34 type=116 (ANGLES) 16 15 18
40: 35 type=116 (ANGLES) 17 15 18
40: 36 type=116 (ANGLES) 15 18 19
40: 37 type=116 (ANGLES) 15 18 20
40: 38 type=116 (ANGLES) 15 18 21
40: 39 type=116 (ANGLES) 19 18 20
40: 40 type=116 (ANGLES) 19 18 21
40: 41 type=116 (ANGLES) 20 18 21
40: 42 type=122 (ANGLES) 4 22 23
40: 43 type=123 (ANGLES) 4 22 24
40: 44 type=124 (ANGLES) 23 22 24
40: 45 type=125 (ANGLES) 22 24 25
40: 46 type=126 (ANGLES) 22 24 26
40: 47 type=127 (ANGLES) 25 24 26
40: 48 type=116 (ANGLES) 24 26 27
40: 49 type=128 (ANGLES) 24 26 28
40: 50 type=129 (ANGLES) 24 26 38
40: 51 type=118 (ANGLES) 27 26 28
40: 52 type=116 (ANGLES) 27 26 38
40: 53 type=119 (ANGLES) 28 26 38
40: 54 type=118 (ANGLES) 26 28 29
40: 55 type=120 (ANGLES) 26 28 30
40: 56 type=120 (ANGLES) 26 28 34
40: 57 type=118 (ANGLES) 29 28 30
40: 58 type=118 (ANGLES) 29 28 34
40: 59 type=120 (ANGLES) 30 28 34
40: 60 type=118 (ANGLES) 28 30 31
40: 61 type=118 (ANGLES) 28 30 32
40: 62 type=118 (ANGLES) 28 30 33
40: 63 type=121 (ANGLES) 31 30 32
40: 64 type=121 (ANGLES) 31 30 33
40: 65 type=121 (ANGLES) 32 30 33
40: 66 type=118 (ANGLES) 28 34 35
40: 67 type=118 (ANGLES) 28 34 36
40: 68 type=118 (ANGLES) 28 34 37
40: 69 type=121 (ANGLES) 35 34 36
40: 70 type=121 (ANGLES) 35 34 37
40: 71 type=121 (ANGLES) 36 34 37
40: 72 type=122 (ANGLES) 26 38 39
40: 73 type=123 (ANGLES) 26 38 40
40: 74 type=124 (ANGLES) 39 38 40
40: 75 type=125 (ANGLES) 38 40 41
40: 76 type=126 (ANGLES) 38 40 42
40: 77 type=127 (ANGLES) 41 40 42
40: 78 type=116 (ANGLES) 40 42 43
40: 79 type=128 (ANGLES) 40 42 44
40: 80 type=129 (ANGLES) 40 42 58
40: 81 type=118 (ANGLES) 43 42 44
40: 82 type=116 (ANGLES) 43 42 58
40: 83 type=119 (ANGLES) 44 42 58
40: 84 type=118 (ANGLES) 42 44 45
40: 85 type=118 (ANGLES) 42 44 46
40: 86 type=130 (ANGLES) 42 44 47
40: 87 type=121 (ANGLES) 45 44 46
40: 88 type=116 (ANGLES) 45 44 47
40: 89 type=116 (ANGLES) 46 44 47
40: 90 type=131 (ANGLES) 44 47 48
40: 91 type=131 (ANGLES) 44 47 50
40: 92 type=132 (ANGLES) 48 47 50
40: 93 type=133 (ANGLES) 47 48 49
40: 94 type=132 (ANGLES) 47 48 52
40: 95 type=133 (ANGLES) 49 48 52
40: 96 type=133 (ANGLES) 47 50 51
40: 97 type=132 (ANGLES) 47 50 54
40: 98 type=133 (ANGLES) 51 50 54
40: 99 type=133 (ANGLES) 48 52 53
40: 100 type=132 (ANGLES) 48 52 56
40: 101 type=133 (ANGLES) 53 52 56
40: 102 type=133 (ANGLES) 50 54 55
40: 103 type=132 (ANGLES) 50 54 56
40: 104 type=133 (ANGLES) 55 54 56
40: 105 type=132 (ANGLES) 52 56 54
40: 106 type=133 (ANGLES) 52 56 57
40: 107 type=133 (ANGLES) 54 56 57
40: 108 type=122 (ANGLES) 42 58 59
40: 109 type=123 (ANGLES) 42 58 60
40: 110 type=124 (ANGLES) 59 58 60
40: 111 type=125 (ANGLES) 58 60 61
40: 112 type=126 (ANGLES) 58 60 62
40: 113 type=127 (ANGLES) 61 60 62
40: 114 type=116 (ANGLES) 60 62 63
40: 115 type=116 (ANGLES) 60 62 64
40: 116 type=129 (ANGLES) 60 62 65
40: 117 type=121 (ANGLES) 63 62 64
40: 118 type=116 (ANGLES) 63 62 65
40: 119 type=116 (ANGLES) 64 62 65
40: 120 type=122 (ANGLES) 62 65 66
40: 121 type=123 (ANGLES) 62 65 67
40: 122 type=124 (ANGLES) 66 65 67
40: 123 type=125 (ANGLES) 65 67 68
40: 124 type=126 (ANGLES) 65 67 69
40: 125 type=127 (ANGLES) 68 67 69
40: 126 type=116 (ANGLES) 67 69 70
40: 127 type=128 (ANGLES) 67 69 71
40: 128 type=129 (ANGLES) 67 69 89
40: 129 type=118 (ANGLES) 70 69 71
40: 130 type=116 (ANGLES) 70 69 89
40: 131 type=119 (ANGLES) 71 69 89
40: 132 type=118 (ANGLES) 69 71 72
40: 133 type=118 (ANGLES) 69 71 73
40: 134 type=120 (ANGLES) 69 71 74
40: 135 type=121 (ANGLES) 72 71 73
40: 136 type=118 (ANGLES) 72 71 74
40: 137 type=118 (ANGLES) 73 71 74
40: 138 type=118 (ANGLES) 71 74 75
40: 139 type=118 (ANGLES) 71 74 76
40: 140 type=120 (ANGLES) 71 74 77
40: 141 type=121 (ANGLES) 75 74 76
40: 142 type=118 (ANGLES) 75 74 77
40: 143 type=118 (ANGLES) 76 74 77
40: 144 type=118 (ANGLES) 74 77 78
40: 145 type=118 (ANGLES) 74 77 79
40: 146 type=117 (ANGLES) 74 77 80
40: 147 type=121 (ANGLES) 78 77 79
40: 148 type=116 (ANGLES) 78 77 80
40: 149 type=116 (ANGLES) 79 77 80
40: 150 type=134 (ANGLES) 77 80 81
40: 151 type=135 (ANGLES) 77 80 82
40: 152 type=133 (ANGLES) 81 80 82
40: 153 type=131 (ANGLES) 80 82 83
40: 154 type=131 (ANGLES) 80 82 86
40: 155 type=131 (ANGLES) 83 82 86
40: 156 type=133 (ANGLES) 82 83 84
40: 157 type=133 (ANGLES) 82 83 85
40: 158 type=133 (ANGLES) 84 83 85
40: 159 type=133 (ANGLES) 82 86 87
40: 160 type=133 (ANGLES) 82 86 88
40: 161 type=133 (ANGLES) 87 86 88
40: 162 type=122 (ANGLES) 69 89 90
40: 163 type=123 (ANGLES) 69 89 91
40: 164 type=124 (ANGLES) 90 89 91
40: 165 type=125 (ANGLES) 89 91 92
40: 166 type=126 (ANGLES) 89 91 93
40: 167 type=127 (ANGLES) 92 91 93
40: 168 type=116 (ANGLES) 91 93 94
40: 169 type=128 (ANGLES) 91 93 95
40: 170 type=129 (ANGLES) 91 93 100
40: 171 type=118 (ANGLES) 94 93 95
40: 172 type=116 (ANGLES) 94 93 100
40: 173 type=119 (ANGLES) 95 93 100
40: 174 type=118 (ANGLES) 93 95 96
40: 175 type=118 (ANGLES) 93 95 97
40: 176 type=136 (ANGLES) 93 95 98
40: 177 type=121 (ANGLES) 96 95 97
40: 178 type=116 (ANGLES) 96 95 98
40: 179 type=116 (ANGLES) 97 95 98
40: 180 type=137 (ANGLES) 95 98 99
40: 181 type=122 (ANGLES) 93 100 101
40: 182 type=123 (ANGLES) 93 100 102
40: 183 type=124 (ANGLES) 101 100 102
40: 184 type=125 (ANGLES) 100 102 103
40: 185 type=126 (ANGLES) 100 102 104
40: 186 type=127 (ANGLES) 103 102 104
40: 187 type=116 (ANGLES) 102 104 105
40: 188 type=128 (ANGLES) 102 104 106
40: 189 type=129 (ANGLES) 102 104 115
40: 190 type=118 (ANGLES) 105 104 106
40: 191 type=116 (ANGLES) 105 104 115
40: 192 type=119 (ANGLES) 106 104 115
40: 193 type=118 (ANGLES) 104 106 107
40: 194 type=118 (ANGLES) 104 106 108
40: 195 type=120 (ANGLES) 104 106 109
40: 196 type=121 (ANGLES) 107 106 108
40: 197 type=118 (ANGLES) 107 106 109
40: 198 type=118 (ANGLES) 108 106 109
40: 199 type=118 (ANGLES) 106 109 110
40: 200 type=118 (ANGLES) 106 109 111
40: 201 type=119 (ANGLES) 106 109 112
40: 202 type=121 (ANGLES) 110 109 111
40: 203 type=116 (ANGLES) 110 109 112
40: 204 type=116 (ANGLES) 111 109 112
40: 205 type=138 (ANGLES) 109 112 113
40: 206 type=138 (ANGLES) 109 112 114
40: 207 type=139 (ANGLES) 113 112 114
40: 208 type=122 (ANGLES) 104 115 116
40: 209 type=123 (ANGLES) 104 115 117
40: 210 type=124 (ANGLES) 116 115 117
40: 211 type=125 (ANGLES) 115 117 118
40: 212 type=126 (ANGLES) 115 117 119
40: 213 type=127 (ANGLES) 118 117 119
40: 214 type=116 (ANGLES) 117 119 120
40: 215 type=128 (ANGLES) 117 119 121
40: 216 type=129 (ANGLES) 117 119 134
40: 217 type=118 (ANGLES) 120 119 121
40: 218 type=116 (ANGLES) 120 119 134
40: 219 type=119 (ANGLES) 121 119 134
40: 220 type=118 (ANGLES) 119 121 122
40: 221 type=118 (ANGLES) 119 121 123
40: 222 type=120 (ANGLES) 119 121 124
40: 223 type=121 (ANGLES) 122 121 123
40: 224 type=118 (ANGLES) 122 121 124
40: 225 type=118 (ANGLES) 123 121 124
40: 226 type=118 (ANGLES) 121 124 125
40: 227 type=120 (ANGLES) 121 124 126
40: 228 type=120 (ANGLES) 121 124 130
40: 229 type=118 (ANGLES) 125 124 126
40: 230 type=118 (ANGLES) 125 124 130
40: 231 type=120 (ANGLES) 126 124 130
40: 232 type=118 (ANGLES) 124 126 127
40: 233 type=118 (ANGLES) 124 126 128
40: 234 type=118 (ANGLES) 124 126 129
40: 235 type=121 (ANGLES) 127 126 128
40: 236 type=121 (ANGLES) 127 126 129
40: 237 type=121 (ANGLES) 128 126 129
40: 238 type=118 (ANGLES) 124 130 131
40: 239 type=118 (ANGLES) 124 130 132
40: 240 type=118 (ANGLES) 124 130 133
40: 241 type=121 (ANGLES) 131 130 132
40: 242 type=121 (ANGLES) 131 130 133
40: 243 type=121 (ANGLES) 132 130 133
40: 244 type=122 (ANGLES) 119 134 135
40: 245 type=123 (ANGLES) 119 134 136
40: 246 type=124 (ANGLES) 135 134 136
40: 247 type=125 (ANGLES) 134 136 137
40: 248 type=126 (ANGLES) 134 136 138
40: 249 type=127 (ANGLES) 137 136 138
40: 250 type=116 (ANGLES) 136 138 139
40: 251 type=128 (ANGLES) 136 138 140
40: 252 type=129 (ANGLES) 136 138 144
40: 253 type=118 (ANGLES) 139 138 140
40: 254 type=116 (ANGLES) 139 138 144
40: 255 type=119 (ANGLES) 140 138 144
40: 256 type=118 (ANGLES) 138 140 141
40: 257 type=118 (ANGLES) 138 140 142
40: 258 type=118 (ANGLES) 138 140 143
40: 259 type=121 (ANGLES) 141 140 142
40: 260 type=121 (ANGLES) 141 140 143
40: 261 type=121 (ANGLES) 142 140 143
40: 262 type=122 (ANGLES) 138 144 145
40: 263 type=123 (ANGLES) 138 144 146
40: 264 type=124 (ANGLES) 145 144 146
40: 265 type=125 (ANGLES) 144 146 147
40: 266 type=126 (ANGLES) 144 146 148
40: 267 type=127 (ANGLES) 147 146 148
40: 268 type=116 (ANGLES) 146 148 149
40: 269 type=128 (ANGLES) 146 148 150
40: 270 type=129 (ANGLES) 146 148 154
40: 271 type=118 (ANGLES) 149 148 150
40: 272 type=116 (ANGLES) 149 148 154
40: 273 type=119 (ANGLES) 150 148 154
40: 274 type=118 (ANGLES) 148 150 151
40: 275 type=118 (ANGLES) 148 150 152
40: 276 type=118 (ANGLES) 148 150 153
40: 277 type=121 (ANGLES) 151 150 152
40: 278 type=121 (ANGLES) 151 150 153
40: 279 type=121 (ANGLES) 152 150 153
40: 280 type=122 (ANGLES) 148 154 155
40: G96Angle:
40: nr: 0
40: Restricted Angles:
40: nr: 0
40: Lin. Angle:
40: nr: 0
40: Bond-Cross:
40: nr: 0
40: BA-Cross:
40: nr: 0
40: U-B:
40: nr: 0
40: Quartic Angles:
40: nr: 0
40: Tab. Angles:
40: nr: 0
40: Proper Dih.:
40: nr: 145
40: iatoms:
40: 0 type=140 (PDIHS) 4 24 22 23
40: 1 type=141 (PDIHS) 22 26 24 25
40: 2 type=140 (PDIHS) 26 40 38 39
40: 3 type=141 (PDIHS) 38 42 40 41
40: 4 type=140 (PDIHS) 42 60 58 59
40: 5 type=142 (PDIHS) 44 47 50 48
40: 6 type=142 (PDIHS) 47 52 48 49
40: 7 type=142 (PDIHS) 47 54 50 51
40: 8 type=142 (PDIHS) 48 56 52 53
40: 9 type=142 (PDIHS) 50 56 54 55
40: 10 type=142 (PDIHS) 52 54 56 57
40: 11 type=141 (PDIHS) 58 62 60 61
40: 12 type=140 (PDIHS) 62 67 65 66
40: 13 type=141 (PDIHS) 65 69 67 68
40: 14 type=140 (PDIHS) 69 91 89 90
40: 15 type=141 (PDIHS) 77 82 80 81
40: 16 type=140 (PDIHS) 80 83 82 86
40: 17 type=141 (PDIHS) 82 84 83 85
40: 18 type=141 (PDIHS) 82 87 86 88
40: 19 type=141 (PDIHS) 89 93 91 92
40: 20 type=140 (PDIHS) 93 102 100 101
40: 21 type=141 (PDIHS) 100 104 102 103
40: 22 type=140 (PDIHS) 104 117 115 116
40: 23 type=140 (PDIHS) 109 113 112 114
40: 24 type=141 (PDIHS) 115 119 117 118
40: 25 type=140 (PDIHS) 119 136 134 135
40: 26 type=141 (PDIHS) 134 138 136 137
40: 27 type=140 (PDIHS) 138 146 144 145
40: 28 type=141 (PDIHS) 144 148 146 147
40: Ryckaert-Bell.:
40: nr: 1565
40: iatoms:
40: 0 type=143 (RBDIHS) 1 0 4 5
40: 1 type=144 (RBDIHS) 1 0 4 6
40: 2 type=144 (RBDIHS) 1 0 4 22
40: 3 type=143 (RBDIHS) 2 0 4 5
40: 4 type=144 (RBDIHS) 2 0 4 6
40: 5 type=144 (RBDIHS) 2 0 4 22
40: 6 type=143 (RBDIHS) 3 0 4 5
40: 7 type=144 (RBDIHS) 3 0 4 6
40: 8 type=144 (RBDIHS) 3 0 4 22
40: 9 type=145 (RBDIHS) 0 4 6 9
40: 10 type=146 (RBDIHS) 22 4 6 9
40: 11 type=147 (RBDIHS) 0 4 6 7
40: 12 type=147 (RBDIHS) 0 4 6 8
40: 13 type=148 (RBDIHS) 5 4 6 7
40: 14 type=148 (RBDIHS) 5 4 6 8
40: 15 type=148 (RBDIHS) 5 4 6 9
40: 16 type=149 (RBDIHS) 22 4 6 7
40: 17 type=149 (RBDIHS) 22 4 6 8
40: 18 type=150 (RBDIHS) 0 4 22 24
40: 19 type=151 (RBDIHS) 6 4 22 24
40: 20 type=148 (RBDIHS) 4 6 9 10
40: 21 type=148 (RBDIHS) 4 6 9 11
40: 22 type=152 (RBDIHS) 4 6 9 12
40: 23 type=148 (RBDIHS) 7 6 9 10
40: 24 type=148 (RBDIHS) 7 6 9 11
40: 25 type=148 (RBDIHS) 7 6 9 12
40: 26 type=148 (RBDIHS) 8 6 9 10
40: 27 type=148 (RBDIHS) 8 6 9 11
40: 28 type=148 (RBDIHS) 8 6 9 12
40: 29 type=148 (RBDIHS) 6 9 12 13
40: 30 type=148 (RBDIHS) 6 9 12 14
40: 31 type=152 (RBDIHS) 6 9 12 15
40: 32 type=148 (RBDIHS) 10 9 12 13
40: 33 type=148 (RBDIHS) 10 9 12 14
40: 34 type=148 (RBDIHS) 10 9 12 15
40: 35 type=148 (RBDIHS) 11 9 12 13
40: 36 type=148 (RBDIHS) 11 9 12 14
40: 37 type=148 (RBDIHS) 11 9 12 15
40: 38 type=148 (RBDIHS) 9 12 15 16
40: 39 type=148 (RBDIHS) 9 12 15 17
40: 40 type=153 (RBDIHS) 9 12 15 18
40: 41 type=148 (RBDIHS) 13 12 15 16
40: 42 type=148 (RBDIHS) 13 12 15 17
40: 43 type=154 (RBDIHS) 13 12 15 18
40: 44 type=148 (RBDIHS) 14 12 15 16
40: 45 type=148 (RBDIHS) 14 12 15 17
40: 46 type=154 (RBDIHS) 14 12 15 18
40: 47 type=144 (RBDIHS) 12 15 18 19
40: 48 type=144 (RBDIHS) 12 15 18 20
40: 49 type=144 (RBDIHS) 12 15 18 21
40: 50 type=143 (RBDIHS) 16 15 18 19
40: 51 type=143 (RBDIHS) 16 15 18 20
40: 52 type=143 (RBDIHS) 16 15 18 21
40: 53 type=143 (RBDIHS) 17 15 18 19
40: 54 type=143 (RBDIHS) 17 15 18 20
40: 55 type=143 (RBDIHS) 17 15 18 21
40: 56 type=155 (RBDIHS) 4 22 24 25
40: 57 type=156 (RBDIHS) 4 22 24 26
40: 58 type=155 (RBDIHS) 23 22 24 25
40: 59 type=157 (RBDIHS) 23 22 24 26
40: 60 type=158 (RBDIHS) 22 24 26 28
40: 61 type=159 (RBDIHS) 22 24 26 38
40: 62 type=160 (RBDIHS) 24 26 28 30
40: 63 type=160 (RBDIHS) 24 26 28 34
40: 64 type=161 (RBDIHS) 38 26 28 30
40: 65 type=161 (RBDIHS) 38 26 28 34
40: 66 type=147 (RBDIHS) 24 26 28 29
40: 67 type=148 (RBDIHS) 27 26 28 29
40: 68 type=148 (RBDIHS) 27 26 28 30
40: 69 type=148 (RBDIHS) 27 26 28 34
40: 70 type=149 (RBDIHS) 38 26 28 29
40: 71 type=150 (RBDIHS) 24 26 38 40
40: 72 type=151 (RBDIHS) 28 26 38 40
40: 73 type=148 (RBDIHS) 26 28 30 31
40: 74 type=148 (RBDIHS) 26 28 30 32
40: 75 type=148 (RBDIHS) 26 28 30 33
40: 76 type=148 (RBDIHS) 29 28 30 31
40: 77 type=148 (RBDIHS) 29 28 30 32
40: 78 type=148 (RBDIHS) 29 28 30 33
40: 79 type=148 (RBDIHS) 34 28 30 31
40: 80 type=148 (RBDIHS) 34 28 30 32
40: 81 type=148 (RBDIHS) 34 28 30 33
40: 82 type=148 (RBDIHS) 26 28 34 35
40: 83 type=148 (RBDIHS) 26 28 34 36
40: 84 type=148 (RBDIHS) 26 28 34 37
40: 85 type=148 (RBDIHS) 29 28 34 35
40: 86 type=148 (RBDIHS) 29 28 34 36
40: 87 type=148 (RBDIHS) 29 28 34 37
40: 88 type=148 (RBDIHS) 30 28 34 35
40: 89 type=148 (RBDIHS) 30 28 34 36
40: 90 type=148 (RBDIHS) 30 28 34 37
40: 91 type=155 (RBDIHS) 26 38 40 41
40: 92 type=156 (RBDIHS) 26 38 40 42
40: 93 type=155 (RBDIHS) 39 38 40 41
40: 94 type=157 (RBDIHS) 39 38 40 42
40: 95 type=158 (RBDIHS) 38 40 42 44
40: 96 type=159 (RBDIHS) 38 40 42 58
40: 97 type=147 (RBDIHS) 40 42 44 45
40: 98 type=147 (RBDIHS) 40 42 44 46
40: 99 type=162 (RBDIHS) 40 42 44 47
40: 100 type=148 (RBDIHS) 43 42 44 45
40: 101 type=148 (RBDIHS) 43 42 44 46
40: 102 type=163 (RBDIHS) 43 42 44 47
40: 103 type=149 (RBDIHS) 58 42 44 45
40: 104 type=149 (RBDIHS) 58 42 44 46
40: 105 type=164 (RBDIHS) 58 42 44 47
40: 106 type=150 (RBDIHS) 40 42 58 60
40: 107 type=151 (RBDIHS) 44 42 58 60
40: 108 type=165 (RBDIHS) 44 47 48 49
40: 109 type=165 (RBDIHS) 44 47 48 52
40: 110 type=165 (RBDIHS) 50 47 48 49
40: 111 type=165 (RBDIHS) 50 47 48 52
40: 112 type=165 (RBDIHS) 44 47 50 51
40: 113 type=165 (RBDIHS) 44 47 50 54
40: 114 type=165 (RBDIHS) 48 47 50 51
40: 115 type=165 (RBDIHS) 48 47 50 54
40: 116 type=165 (RBDIHS) 47 48 52 53
40: 117 type=165 (RBDIHS) 47 48 52 56
40: 118 type=165 (RBDIHS) 49 48 52 53
40: 119 type=165 (RBDIHS) 49 48 52 56
40: 120 type=165 (RBDIHS) 47 50 54 55
40: 121 type=165 (RBDIHS) 47 50 54 56
40: 122 type=165 (RBDIHS) 51 50 54 55
40: 123 type=165 (RBDIHS) 51 50 54 56
40: 124 type=165 (RBDIHS) 48 52 56 54
40: 125 type=165 (RBDIHS) 48 52 56 57
40: 126 type=165 (RBDIHS) 53 52 56 54
40: 127 type=165 (RBDIHS) 53 52 56 57
40: 128 type=165 (RBDIHS) 50 54 56 52
40: 129 type=165 (RBDIHS) 50 54 56 57
40: 130 type=165 (RBDIHS) 55 54 56 52
40: 131 type=165 (RBDIHS) 55 54 56 57
40: 132 type=155 (RBDIHS) 42 58 60 61
40: 133 type=156 (RBDIHS) 42 58 60 62
40: 134 type=155 (RBDIHS) 59 58 60 61
40: 135 type=157 (RBDIHS) 59 58 60 62
40: 136 type=159 (RBDIHS) 58 60 62 65
40: 137 type=150 (RBDIHS) 60 62 65 67
40: 138 type=155 (RBDIHS) 62 65 67 68
40: 139 type=156 (RBDIHS) 62 65 67 69
40: 140 type=155 (RBDIHS) 66 65 67 68
40: 141 type=157 (RBDIHS) 66 65 67 69
40: 142 type=158 (RBDIHS) 65 67 69 71
40: 143 type=159 (RBDIHS) 65 67 69 89
40: 144 type=166 (RBDIHS) 67 69 71 74
40: 145 type=167 (RBDIHS) 89 69 71 74
40: 146 type=147 (RBDIHS) 67 69 71 72
40: 147 type=147 (RBDIHS) 67 69 71 73
40: 148 type=148 (RBDIHS) 70 69 71 72
40: 149 type=148 (RBDIHS) 70 69 71 73
40: 150 type=148 (RBDIHS) 70 69 71 74
40: 151 type=149 (RBDIHS) 89 69 71 72
40: 152 type=149 (RBDIHS) 89 69 71 73
40: 153 type=150 (RBDIHS) 67 69 89 91
40: 154 type=151 (RBDIHS) 71 69 89 91
40: 155 type=148 (RBDIHS) 69 71 74 75
40: 156 type=148 (RBDIHS) 69 71 74 76
40: 157 type=152 (RBDIHS) 69 71 74 77
40: 158 type=148 (RBDIHS) 72 71 74 75
40: 159 type=148 (RBDIHS) 72 71 74 76
40: 160 type=148 (RBDIHS) 72 71 74 77
40: 161 type=148 (RBDIHS) 73 71 74 75
40: 162 type=148 (RBDIHS) 73 71 74 76
40: 163 type=148 (RBDIHS) 73 71 74 77
40: 164 type=148 (RBDIHS) 71 74 77 78
40: 165 type=148 (RBDIHS) 71 74 77 79
40: 166 type=153 (RBDIHS) 71 74 77 80
40: 167 type=148 (RBDIHS) 75 74 77 78
40: 168 type=148 (RBDIHS) 75 74 77 79
40: 169 type=168 (RBDIHS) 75 74 77 80
40: 170 type=148 (RBDIHS) 76 74 77 78
40: 171 type=148 (RBDIHS) 76 74 77 79
40: 172 type=168 (RBDIHS) 76 74 77 80
40: 173 type=169 (RBDIHS) 74 77 80 81
40: 174 type=170 (RBDIHS) 74 77 80 82
40: 175 type=171 (RBDIHS) 78 77 80 82
40: 176 type=171 (RBDIHS) 79 77 80 82
40: 177 type=172 (RBDIHS) 77 80 82 83
40: 178 type=172 (RBDIHS) 77 80 82 86
40: 179 type=173 (RBDIHS) 81 80 82 83
40: 180 type=173 (RBDIHS) 81 80 82 86
40: 181 type=173 (RBDIHS) 80 82 83 84
40: 182 type=173 (RBDIHS) 80 82 83 85
40: 183 type=173 (RBDIHS) 86 82 83 84
40: 184 type=173 (RBDIHS) 86 82 83 85
40: 185 type=173 (RBDIHS) 80 82 86 87
40: 186 type=173 (RBDIHS) 80 82 86 88
40: 187 type=173 (RBDIHS) 83 82 86 87
40: 188 type=173 (RBDIHS) 83 82 86 88
40: 189 type=155 (RBDIHS) 69 89 91 92
40: 190 type=156 (RBDIHS) 69 89 91 93
40: 191 type=155 (RBDIHS) 90 89 91 92
40: 192 type=157 (RBDIHS) 90 89 91 93
40: 193 type=158 (RBDIHS) 89 91 93 95
40: 194 type=159 (RBDIHS) 89 91 93 100
40: 195 type=174 (RBDIHS) 91 93 95 98
40: 196 type=175 (RBDIHS) 100 93 95 98
40: 197 type=147 (RBDIHS) 91 93 95 96
40: 198 type=147 (RBDIHS) 91 93 95 97
40: 199 type=148 (RBDIHS) 94 93 95 96
40: 200 type=148 (RBDIHS) 94 93 95 97
40: 201 type=176 (RBDIHS) 94 93 95 98
40: 202 type=149 (RBDIHS) 100 93 95 96
40: 203 type=149 (RBDIHS) 100 93 95 97
40: 204 type=150 (RBDIHS) 91 93 100 102
40: 205 type=151 (RBDIHS) 95 93 100 102
40: 206 type=177 (RBDIHS) 93 95 98 99
40: 207 type=178 (RBDIHS) 96 95 98 99
40: 208 type=178 (RBDIHS) 97 95 98 99
40: 209 type=155 (RBDIHS) 93 100 102 103
40: 210 type=156 (RBDIHS) 93 100 102 104
40: 211 type=155 (RBDIHS) 101 100 102 103
40: 212 type=157 (RBDIHS) 101 100 102 104
40: 213 type=158 (RBDIHS) 100 102 104 106
40: 214 type=159 (RBDIHS) 100 102 104 115
40: 215 type=179 (RBDIHS) 102 104 106 109
40: 216 type=180 (RBDIHS) 115 104 106 109
40: 217 type=147 (RBDIHS) 102 104 106 107
40: 218 type=147 (RBDIHS) 102 104 106 108
40: 219 type=148 (RBDIHS) 105 104 106 107
40: 220 type=148 (RBDIHS) 105 104 106 108
40: 221 type=148 (RBDIHS) 105 104 106 109
40: 222 type=149 (RBDIHS) 115 104 106 107
40: 223 type=149 (RBDIHS) 115 104 106 108
40: 224 type=150 (RBDIHS) 102 104 115 117
40: 225 type=151 (RBDIHS) 106 104 115 117
40: 226 type=148 (RBDIHS) 104 106 109 110
40: 227 type=148 (RBDIHS) 104 106 109 111
40: 228 type=181 (RBDIHS) 104 106 109 112
40: 229 type=148 (RBDIHS) 107 106 109 110
40: 230 type=148 (RBDIHS) 107 106 109 111
40: 231 type=182 (RBDIHS) 107 106 109 112
40: 232 type=148 (RBDIHS) 108 106 109 110
40: 233 type=148 (RBDIHS) 108 106 109 111
40: 234 type=182 (RBDIHS) 108 106 109 112
40: 235 type=183 (RBDIHS) 106 109 112 113
40: 236 type=183 (RBDIHS) 106 109 112 114
40: 237 type=155 (RBDIHS) 104 115 117 118
40: 238 type=156 (RBDIHS) 104 115 117 119
40: 239 type=155 (RBDIHS) 116 115 117 118
40: 240 type=157 (RBDIHS) 116 115 117 119
40: 241 type=158 (RBDIHS) 115 117 119 121
40: 242 type=159 (RBDIHS) 115 117 119 134
40: 243 type=184 (RBDIHS) 117 119 121 124
40: 244 type=185 (RBDIHS) 134 119 121 124
40: 245 type=147 (RBDIHS) 117 119 121 122
40: 246 type=147 (RBDIHS) 117 119 121 123
40: 247 type=148 (RBDIHS) 120 119 121 122
40: 248 type=148 (RBDIHS) 120 119 121 123
40: 249 type=148 (RBDIHS) 120 119 121 124
40: 250 type=149 (RBDIHS) 134 119 121 122
40: 251 type=149 (RBDIHS) 134 119 121 123
40: 252 type=150 (RBDIHS) 117 119 134 136
40: 253 type=151 (RBDIHS) 121 119 134 136
40: 254 type=148 (RBDIHS) 119 121 124 125
40: 255 type=152 (RBDIHS) 119 121 124 126
40: 256 type=152 (RBDIHS) 119 121 124 130
40: 257 type=148 (RBDIHS) 122 121 124 125
40: 258 type=148 (RBDIHS) 122 121 124 126
40: 259 type=148 (RBDIHS) 122 121 124 130
40: 260 type=148 (RBDIHS) 123 121 124 125
40: 261 type=148 (RBDIHS) 123 121 124 126
40: 262 type=148 (RBDIHS) 123 121 124 130
40: 263 type=148 (RBDIHS) 121 124 126 127
40: 264 type=148 (RBDIHS) 121 124 126 128
40: 265 type=148 (RBDIHS) 121 124 126 129
40: 266 type=148 (RBDIHS) 125 124 126 127
40: 267 type=148 (RBDIHS) 125 124 126 128
40: 268 type=148 (RBDIHS) 125 124 126 129
40: 269 type=148 (RBDIHS) 130 124 126 127
40: 270 type=148 (RBDIHS) 130 124 126 128
40: 271 type=148 (RBDIHS) 130 124 126 129
40: 272 type=148 (RBDIHS) 121 124 130 131
40: 273 type=148 (RBDIHS) 121 124 130 132
40: 274 type=148 (RBDIHS) 121 124 130 133
40: 275 type=148 (RBDIHS) 125 124 130 131
40: 276 type=148 (RBDIHS) 125 124 130 132
40: 277 type=148 (RBDIHS) 125 124 130 133
40: 278 type=148 (RBDIHS) 126 124 130 131
40: 279 type=148 (RBDIHS) 126 124 130 132
40: 280 type=148 (RBDIHS) 126 124 130 133
40: 281 type=155 (RBDIHS) 119 134 136 137
40: 282 type=156 (RBDIHS) 119 134 136 138
40: 283 type=155 (RBDIHS) 135 134 136 137
40: 284 type=157 (RBDIHS) 135 134 136 138
40: 285 type=158 (RBDIHS) 134 136 138 140
40: 286 type=159 (RBDIHS) 134 136 138 144
40: 287 type=147 (RBDIHS) 136 138 140 141
40: 288 type=147 (RBDIHS) 136 138 140 142
40: 289 type=147 (RBDIHS) 136 138 140 143
40: 290 type=148 (RBDIHS) 139 138 140 141
40: 291 type=148 (RBDIHS) 139 138 140 142
40: 292 type=148 (RBDIHS) 139 138 140 143
40: 293 type=149 (RBDIHS) 144 138 140 141
40: 294 type=149 (RBDIHS) 144 138 140 142
40: 295 type=149 (RBDIHS) 144 138 140 143
40: 296 type=150 (RBDIHS) 136 138 144 146
40: 297 type=151 (RBDIHS) 140 138 144 146
40: 298 type=155 (RBDIHS) 138 144 146 147
40: 299 type=156 (RBDIHS) 138 144 146 148
40: 300 type=155 (RBDIHS) 145 144 146 147
40: 301 type=157 (RBDIHS) 145 144 146 148
40: 302 type=158 (RBDIHS) 144 146 148 150
40: 303 type=159 (RBDIHS) 144 146 148 154
40: 304 type=147 (RBDIHS) 146 148 150 151
40: 305 type=147 (RBDIHS) 146 148 150 152
40: 306 type=147 (RBDIHS) 146 148 150 153
40: 307 type=148 (RBDIHS) 149 148 150 151
40: 308 type=148 (RBDIHS) 149 148 150 152
40: 309 type=148 (RBDIHS) 149 148 150 153
40: 310 type=149 (RBDIHS) 154 148 150 151
40: 311 type=149 (RBDIHS) 154 148 150 152
40: 312 type=149 (RBDIHS) 154 148 150 153
40: Restricted Dih.:
40: nr: 0
40: CBT Dih.:
40: nr: 0
40: Fourier Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Tab. Dih.:
40: nr: 0
40: CMAP Dih.:
40: nr: 0
40: GB 1-2 Pol. (unused):
40: nr: 0
40: GB 1-3 Pol. (unused):
40: nr: 0
40: GB 1-4 Pol. (unused):
40: nr: 0
40: GB Polarization (unused):
40: nr: 0
40: Nonpolar Sol. (unused):
40: nr: 0
40: LJ-14:
40: nr: 1197
40: iatoms:
40: 0 type=186 (LJ14) 0 7
40: 1 type=186 (LJ14) 0 8
40: 2 type=187 (LJ14) 0 9
40: 3 type=188 (LJ14) 0 23
40: 4 type=189 (LJ14) 0 24
40: 5 type=190 (LJ14) 1 5
40: 6 type=190 (LJ14) 1 6
40: 7 type=190 (LJ14) 1 22
40: 8 type=190 (LJ14) 2 5
40: 9 type=190 (LJ14) 2 6
40: 10 type=190 (LJ14) 2 22
40: 11 type=190 (LJ14) 3 5
40: 12 type=190 (LJ14) 3 6
40: 13 type=190 (LJ14) 3 22
40: 14 type=191 (LJ14) 4 10
40: 15 type=191 (LJ14) 4 11
40: 16 type=192 (LJ14) 4 12
40: 17 type=190 (LJ14) 4 25
40: 18 type=192 (LJ14) 4 26
40: 19 type=193 (LJ14) 5 7
40: 20 type=193 (LJ14) 5 8
40: 21 type=191 (LJ14) 5 9
40: 22 type=194 (LJ14) 5 23
40: 23 type=186 (LJ14) 5 24
40: 24 type=191 (LJ14) 6 13
40: 25 type=191 (LJ14) 6 14
40: 26 type=192 (LJ14) 6 15
40: 27 type=195 (LJ14) 6 23
40: 28 type=187 (LJ14) 6 24
40: 29 type=193 (LJ14) 7 10
40: 30 type=193 (LJ14) 7 11
40: 31 type=191 (LJ14) 7 12
40: 32 type=196 (LJ14) 7 22
40: 33 type=193 (LJ14) 8 10
40: 34 type=193 (LJ14) 8 11
40: 35 type=191 (LJ14) 8 12
40: 36 type=196 (LJ14) 8 22
40: 37 type=191 (LJ14) 9 16
40: 38 type=191 (LJ14) 9 17
40: 39 type=187 (LJ14) 9 18
40: 40 type=197 (LJ14) 9 22
40: 41 type=193 (LJ14) 10 13
40: 42 type=193 (LJ14) 10 14
40: 43 type=191 (LJ14) 10 15
40: 44 type=193 (LJ14) 11 13
40: 45 type=193 (LJ14) 11 14
40: 46 type=191 (LJ14) 11 15
40: 47 type=190 (LJ14) 12 19
40: 48 type=190 (LJ14) 12 20
40: 49 type=190 (LJ14) 12 21
40: 50 type=193 (LJ14) 13 16
40: 51 type=193 (LJ14) 13 17
40: 52 type=186 (LJ14) 13 18
40: 53 type=193 (LJ14) 14 16
40: 54 type=193 (LJ14) 14 17
40: 55 type=186 (LJ14) 14 18
40: 56 type=190 (LJ14) 16 19
40: 57 type=190 (LJ14) 16 20
40: 58 type=190 (LJ14) 16 21
40: 59 type=190 (LJ14) 17 19
40: 60 type=190 (LJ14) 17 20
40: 61 type=190 (LJ14) 17 21
40: 62 type=196 (LJ14) 22 27
40: 63 type=197 (LJ14) 22 28
40: 64 type=198 (LJ14) 22 38
40: 65 type=190 (LJ14) 23 25
40: 66 type=195 (LJ14) 23 26
40: 67 type=186 (LJ14) 24 29
40: 68 type=187 (LJ14) 24 30
40: 69 type=187 (LJ14) 24 34
40: 70 type=188 (LJ14) 24 39
40: 71 type=189 (LJ14) 24 40
40: 72 type=190 (LJ14) 25 27
40: 73 type=190 (LJ14) 25 28
40: 74 type=190 (LJ14) 25 38
40: 75 type=191 (LJ14) 26 31
40: 76 type=191 (LJ14) 26 32
40: 77 type=191 (LJ14) 26 33
40: 78 type=191 (LJ14) 26 35
40: 79 type=191 (LJ14) 26 36
40: 80 type=191 (LJ14) 26 37
40: 81 type=190 (LJ14) 26 41
40: 82 type=192 (LJ14) 26 42
40: 83 type=193 (LJ14) 27 29
40: 84 type=191 (LJ14) 27 30
40: 85 type=191 (LJ14) 27 34
40: 86 type=194 (LJ14) 27 39
40: 87 type=186 (LJ14) 27 40
40: 88 type=195 (LJ14) 28 39
40: 89 type=187 (LJ14) 28 40
40: 90 type=193 (LJ14) 29 31
40: 91 type=193 (LJ14) 29 32
40: 92 type=193 (LJ14) 29 33
40: 93 type=193 (LJ14) 29 35
40: 94 type=193 (LJ14) 29 36
40: 95 type=193 (LJ14) 29 37
40: 96 type=196 (LJ14) 29 38
40: 97 type=191 (LJ14) 30 35
40: 98 type=191 (LJ14) 30 36
40: 99 type=191 (LJ14) 30 37
40: 100 type=197 (LJ14) 30 38
40: 101 type=191 (LJ14) 31 34
40: 102 type=191 (LJ14) 32 34
40: 103 type=191 (LJ14) 33 34
40: 104 type=197 (LJ14) 34 38
40: 105 type=196 (LJ14) 38 43
40: 106 type=197 (LJ14) 38 44
40: 107 type=198 (LJ14) 38 58
40: 108 type=190 (LJ14) 39 41
40: 109 type=195 (LJ14) 39 42
40: 110 type=186 (LJ14) 40 45
40: 111 type=186 (LJ14) 40 46
40: 112 type=199 (LJ14) 40 47
40: 113 type=188 (LJ14) 40 59
40: 114 type=189 (LJ14) 40 60
40: 115 type=190 (LJ14) 41 43
40: 116 type=190 (LJ14) 41 44
40: 117 type=190 (LJ14) 41 58
40: 118 type=200 (LJ14) 42 48
40: 119 type=200 (LJ14) 42 50
40: 120 type=190 (LJ14) 42 61
40: 121 type=192 (LJ14) 42 62
40: 122 type=193 (LJ14) 43 45
40: 123 type=193 (LJ14) 43 46
40: 124 type=201 (LJ14) 43 47
40: 125 type=194 (LJ14) 43 59
40: 126 type=186 (LJ14) 43 60
40: 127 type=202 (LJ14) 44 49
40: 128 type=202 (LJ14) 44 51
40: 129 type=200 (LJ14) 44 52
40: 130 type=200 (LJ14) 44 54
40: 131 type=195 (LJ14) 44 59
40: 132 type=187 (LJ14) 44 60
40: 133 type=201 (LJ14) 45 48
40: 134 type=201 (LJ14) 45 50
40: 135 type=196 (LJ14) 45 58
40: 136 type=201 (LJ14) 46 48
40: 137 type=201 (LJ14) 46 50
40: 138 type=196 (LJ14) 46 58
40: 139 type=203 (LJ14) 47 53
40: 140 type=203 (LJ14) 47 55
40: 141 type=204 (LJ14) 47 56
40: 142 type=205 (LJ14) 47 58
40: 143 type=203 (LJ14) 48 51
40: 144 type=204 (LJ14) 48 54
40: 145 type=203 (LJ14) 48 57
40: 146 type=203 (LJ14) 49 50
40: 147 type=206 (LJ14) 49 53
40: 148 type=203 (LJ14) 49 56
40: 149 type=204 (LJ14) 50 52
40: 150 type=203 (LJ14) 50 57
40: 151 type=206 (LJ14) 51 55
40: 152 type=203 (LJ14) 51 56
40: 153 type=203 (LJ14) 52 55
40: 154 type=203 (LJ14) 53 54
40: 155 type=206 (LJ14) 53 57
40: 156 type=206 (LJ14) 55 57
40: 157 type=196 (LJ14) 58 63
40: 158 type=196 (LJ14) 58 64
40: 159 type=198 (LJ14) 58 65
40: 160 type=190 (LJ14) 59 61
40: 161 type=195 (LJ14) 59 62
40: 162 type=188 (LJ14) 60 66
40: 163 type=189 (LJ14) 60 67
40: 164 type=190 (LJ14) 61 63
40: 165 type=190 (LJ14) 61 64
40: 166 type=190 (LJ14) 61 65
40: 167 type=190 (LJ14) 62 68
40: 168 type=192 (LJ14) 62 69
40: 169 type=194 (LJ14) 63 66
40: 170 type=186 (LJ14) 63 67
40: 171 type=194 (LJ14) 64 66
40: 172 type=186 (LJ14) 64 67
40: 173 type=196 (LJ14) 65 70
40: 174 type=197 (LJ14) 65 71
40: 175 type=198 (LJ14) 65 89
40: 176 type=190 (LJ14) 66 68
40: 177 type=195 (LJ14) 66 69
40: 178 type=186 (LJ14) 67 72
40: 179 type=186 (LJ14) 67 73
40: 180 type=187 (LJ14) 67 74
40: 181 type=188 (LJ14) 67 90
40: 182 type=189 (LJ14) 67 91
40: 183 type=190 (LJ14) 68 70
40: 184 type=190 (LJ14) 68 71
40: 185 type=190 (LJ14) 68 89
40: 186 type=191 (LJ14) 69 75
40: 187 type=191 (LJ14) 69 76
40: 188 type=192 (LJ14) 69 77
40: 189 type=190 (LJ14) 69 92
40: 190 type=192 (LJ14) 69 93
40: 191 type=193 (LJ14) 70 72
40: 192 type=193 (LJ14) 70 73
40: 193 type=191 (LJ14) 70 74
40: 194 type=194 (LJ14) 70 90
40: 195 type=186 (LJ14) 70 91
40: 196 type=191 (LJ14) 71 78
40: 197 type=191 (LJ14) 71 79
40: 198 type=187 (LJ14) 71 80
40: 199 type=195 (LJ14) 71 90
40: 200 type=187 (LJ14) 71 91
40: 201 type=193 (LJ14) 72 75
40: 202 type=193 (LJ14) 72 76
40: 203 type=191 (LJ14) 72 77
40: 204 type=196 (LJ14) 72 89
40: 205 type=193 (LJ14) 73 75
40: 206 type=193 (LJ14) 73 76
40: 207 type=191 (LJ14) 73 77
40: 208 type=196 (LJ14) 73 89
40: 209 type=190 (LJ14) 74 81
40: 210 type=207 (LJ14) 74 82
40: 211 type=197 (LJ14) 74 89
40: 212 type=193 (LJ14) 75 78
40: 213 type=193 (LJ14) 75 79
40: 214 type=186 (LJ14) 75 80
40: 215 type=193 (LJ14) 76 78
40: 216 type=193 (LJ14) 76 79
40: 217 type=186 (LJ14) 76 80
40: 218 type=187 (LJ14) 77 83
40: 219 type=187 (LJ14) 77 86
40: 220 type=190 (LJ14) 78 81
40: 221 type=208 (LJ14) 78 82
40: 222 type=190 (LJ14) 79 81
40: 223 type=208 (LJ14) 79 82
40: 224 type=190 (LJ14) 80 84
40: 225 type=190 (LJ14) 80 85
40: 226 type=190 (LJ14) 80 87
40: 227 type=190 (LJ14) 80 88
40: 228 type=190 (LJ14) 81 83
40: 229 type=190 (LJ14) 81 86
40: 230 type=190 (LJ14) 83 87
40: 231 type=190 (LJ14) 83 88
40: 232 type=190 (LJ14) 84 86
40: 233 type=190 (LJ14) 85 86
40: 234 type=196 (LJ14) 89 94
40: 235 type=197 (LJ14) 89 95
40: 236 type=198 (LJ14) 89 100
40: 237 type=190 (LJ14) 90 92
40: 238 type=195 (LJ14) 90 93
40: 239 type=186 (LJ14) 91 96
40: 240 type=186 (LJ14) 91 97
40: 241 type=209 (LJ14) 91 98
40: 242 type=188 (LJ14) 91 101
40: 243 type=189 (LJ14) 91 102
40: 244 type=190 (LJ14) 92 94
40: 245 type=190 (LJ14) 92 95
40: 246 type=190 (LJ14) 92 100
40: 247 type=190 (LJ14) 93 99
40: 248 type=190 (LJ14) 93 103
40: 249 type=192 (LJ14) 93 104
40: 250 type=193 (LJ14) 94 96
40: 251 type=193 (LJ14) 94 97
40: 252 type=210 (LJ14) 94 98
40: 253 type=194 (LJ14) 94 101
40: 254 type=186 (LJ14) 94 102
40: 255 type=195 (LJ14) 95 101
40: 256 type=187 (LJ14) 95 102
40: 257 type=190 (LJ14) 96 99
40: 258 type=196 (LJ14) 96 100
40: 259 type=190 (LJ14) 97 99
40: 260 type=196 (LJ14) 97 100
40: 261 type=211 (LJ14) 98 100
40: 262 type=196 (LJ14) 100 105
40: 263 type=197 (LJ14) 100 106
40: 264 type=198 (LJ14) 100 115
40: 265 type=190 (LJ14) 101 103
40: 266 type=195 (LJ14) 101 104
40: 267 type=186 (LJ14) 102 107
40: 268 type=186 (LJ14) 102 108
40: 269 type=187 (LJ14) 102 109
40: 270 type=188 (LJ14) 102 116
40: 271 type=189 (LJ14) 102 117
40: 272 type=190 (LJ14) 103 105
40: 273 type=190 (LJ14) 103 106
40: 274 type=190 (LJ14) 103 115
40: 275 type=191 (LJ14) 104 110
40: 276 type=191 (LJ14) 104 111
40: 277 type=197 (LJ14) 104 112
40: 278 type=190 (LJ14) 104 118
40: 279 type=192 (LJ14) 104 119
40: 280 type=193 (LJ14) 105 107
40: 281 type=193 (LJ14) 105 108
40: 282 type=191 (LJ14) 105 109
40: 283 type=194 (LJ14) 105 116
40: 284 type=186 (LJ14) 105 117
40: 285 type=195 (LJ14) 106 113
40: 286 type=195 (LJ14) 106 114
40: 287 type=195 (LJ14) 106 116
40: 288 type=187 (LJ14) 106 117
40: 289 type=193 (LJ14) 107 110
40: 290 type=193 (LJ14) 107 111
40: 291 type=196 (LJ14) 107 112
40: 292 type=196 (LJ14) 107 115
40: 293 type=193 (LJ14) 108 110
40: 294 type=193 (LJ14) 108 111
40: 295 type=196 (LJ14) 108 112
40: 296 type=196 (LJ14) 108 115
40: 297 type=197 (LJ14) 109 115
40: 298 type=194 (LJ14) 110 113
40: 299 type=194 (LJ14) 110 114
40: 300 type=194 (LJ14) 111 113
40: 301 type=194 (LJ14) 111 114
40: 302 type=196 (LJ14) 115 120
40: 303 type=197 (LJ14) 115 121
40: 304 type=198 (LJ14) 115 134
40: 305 type=190 (LJ14) 116 118
40: 306 type=195 (LJ14) 116 119
40: 307 type=186 (LJ14) 117 122
40: 308 type=186 (LJ14) 117 123
40: 309 type=187 (LJ14) 117 124
40: 310 type=188 (LJ14) 117 135
40: 311 type=189 (LJ14) 117 136
40: 312 type=190 (LJ14) 118 120
40: 313 type=190 (LJ14) 118 121
40: 314 type=190 (LJ14) 118 134
40: 315 type=191 (LJ14) 119 125
40: 316 type=192 (LJ14) 119 126
40: 317 type=192 (LJ14) 119 130
40: 318 type=190 (LJ14) 119 137
40: 319 type=192 (LJ14) 119 138
40: 320 type=193 (LJ14) 120 122
40: 321 type=193 (LJ14) 120 123
40: 322 type=191 (LJ14) 120 124
40: 323 type=194 (LJ14) 120 135
40: 324 type=186 (LJ14) 120 136
40: 325 type=191 (LJ14) 121 127
40: 326 type=191 (LJ14) 121 128
40: 327 type=191 (LJ14) 121 129
40: 328 type=191 (LJ14) 121 131
40: 329 type=191 (LJ14) 121 132
40: 330 type=191 (LJ14) 121 133
40: 331 type=195 (LJ14) 121 135
40: 332 type=187 (LJ14) 121 136
40: 333 type=193 (LJ14) 122 125
40: 334 type=191 (LJ14) 122 126
40: 335 type=191 (LJ14) 122 130
40: 336 type=196 (LJ14) 122 134
40: 337 type=193 (LJ14) 123 125
40: 338 type=191 (LJ14) 123 126
40: 339 type=191 (LJ14) 123 130
40: 340 type=196 (LJ14) 123 134
40: 341 type=197 (LJ14) 124 134
40: 342 type=193 (LJ14) 125 127
40: 343 type=193 (LJ14) 125 128
40: 344 type=193 (LJ14) 125 129
40: 345 type=193 (LJ14) 125 131
40: 346 type=193 (LJ14) 125 132
40: 347 type=193 (LJ14) 125 133
40: 348 type=191 (LJ14) 126 131
40: 349 type=191 (LJ14) 126 132
40: 350 type=191 (LJ14) 126 133
40: 351 type=191 (LJ14) 127 130
40: 352 type=191 (LJ14) 128 130
40: 353 type=191 (LJ14) 129 130
40: 354 type=196 (LJ14) 134 139
40: 355 type=197 (LJ14) 134 140
40: 356 type=198 (LJ14) 134 144
40: 357 type=190 (LJ14) 135 137
40: 358 type=195 (LJ14) 135 138
40: 359 type=186 (LJ14) 136 141
40: 360 type=186 (LJ14) 136 142
40: 361 type=186 (LJ14) 136 143
40: 362 type=188 (LJ14) 136 145
40: 363 type=189 (LJ14) 136 146
40: 364 type=190 (LJ14) 137 139
40: 365 type=190 (LJ14) 137 140
40: 366 type=190 (LJ14) 137 144
40: 367 type=190 (LJ14) 138 147
40: 368 type=192 (LJ14) 138 148
40: 369 type=193 (LJ14) 139 141
40: 370 type=193 (LJ14) 139 142
40: 371 type=193 (LJ14) 139 143
40: 372 type=194 (LJ14) 139 145
40: 373 type=186 (LJ14) 139 146
40: 374 type=195 (LJ14) 140 145
40: 375 type=187 (LJ14) 140 146
40: 376 type=196 (LJ14) 141 144
40: 377 type=196 (LJ14) 142 144
40: 378 type=196 (LJ14) 143 144
40: 379 type=196 (LJ14) 144 149
40: 380 type=197 (LJ14) 144 150
40: 381 type=198 (LJ14) 144 154
40: 382 type=190 (LJ14) 145 147
40: 383 type=195 (LJ14) 145 148
40: 384 type=186 (LJ14) 146 151
40: 385 type=186 (LJ14) 146 152
40: 386 type=186 (LJ14) 146 153
40: 387 type=188 (LJ14) 146 155
40: 388 type=190 (LJ14) 147 149
40: 389 type=190 (LJ14) 147 150
40: 390 type=190 (LJ14) 147 154
40: 391 type=193 (LJ14) 149 151
40: 392 type=193 (LJ14) 149 152
40: 393 type=193 (LJ14) 149 153
40: 394 type=194 (LJ14) 149 155
40: 395 type=195 (LJ14) 150 155
40: 396 type=196 (LJ14) 151 154
40: 397 type=196 (LJ14) 152 154
40: 398 type=196 (LJ14) 153 154
40: Coulomb-14:
40: nr: 0
40: LJC-14 q:
40: nr: 0
40: LJC Pairs NB:
40: nr: 0
40: LJ (SR):
40: nr: 0
40: Buck.ham (SR):
40: nr: 0
40: LJ (unused):
40: nr: 0
40: B.ham (unused):
40: nr: 0
40: Disper. corr.:
40: nr: 0
40: Coulomb (SR):
40: nr: 0
40: Coul (unused):
40: nr: 0
40: RF excl.:
40: nr: 0
40: Coul. recip.:
40: nr: 0
40: LJ recip.:
40: nr: 0
40: DPD:
40: nr: 0
40: Polarization:
40: nr: 0
40: Water Pol.:
40: nr: 0
40: Thole Pol.:
40: nr: 0
40: Anharm. Pol.:
40: nr: 0
40: Position Rest.:
40: nr: 0
40: Flat-bottom posres:
40: nr: 0
40: Dis. Rest.:
40: nr: 0
40: D.R.Viol. (nm):
40: nr: 0
40: Orient. Rest.:
40: nr: 0
40: Ori. R. RMSD:
40: nr: 0
40: Angle Rest.:
40: nr: 0
40: Angle Rest. Z:
40: nr: 0
40: Dih. Rest.:
40: nr: 0
40: Dih. Rest. Viol.:
40: nr: 0
40: Constraint:
40: nr: 0
40: Constr. No Conn.:
40: nr: 0
40: Settle:
40: nr: 0
40: Virtual site 2:
40: nr: 0
40: Virtual site 2fd:
40: nr: 0
40: Virtual site 3:
40: nr: 0
40: Virtual site 3fd:
40: nr: 0
40: Virtual site 3fad:
40: nr: 0
40: Virtual site 3out:
40: nr: 0
40: Virtual site 4fd:
40: nr: 0
40: Virtual site 4fdn:
40: nr: 0
40: Virtual site N:
40: nr: 0
40: COM Pull En.:
40: nr: 0
40: Density fitting:
40: nr: 0
40: Quantum En.:
40: nr: 0
40: Potential:
40: nr: 0
40: Kinetic En.:
40: nr: 0
40: Total Energy:
40: nr: 0
40: Conserved En.:
40: nr: 0
40: Temperature:
40: nr: 0
40: Vir. Temp. (not used):
40: nr: 0
40: Pres. DC:
40: nr: 0
40: Pressure:
40: nr: 0
40: dH/dl constr.:
40: nr: 0
40: dVremain/dl:
40: nr: 0
40: dEkin/dl:
40: nr: 0
40: dVcoul/dl:
40: nr: 0
40: dVvdw/dl:
40: nr: 0
40: dVbonded/dl:
40: nr: 0
40: dVrestraint/dl:
40: nr: 0
40: dVtemperature/dl:
40: nr: 0
40: grp[T-Coupling ] nr=1, name=[ rest]
40: grp[Energy Mon. ] nr=1, name=[ rest]
40: grp[Acceleration] nr=1, name=[ rest]
40: grp[Freeze ] nr=1, name=[ rest]
40: grp[User1 ] nr=1, name=[ rest]
40: grp[User2 ] nr=1, name=[ rest]
40: grp[VCM ] nr=1, name=[ rest]
40: grp[Compressed X] nr=1, name=[ rest]
40: grp[Or. Res. Fit] nr=1, name=[ rest]
40: grp[QMMM ] nr=1, name=[ rest]
40: grpname (11):
40: grpname[0]={name="System"}
40: grpname[1]={name="Protein"}
40: grpname[2]={name="Protein-H"}
40: grpname[3]={name="C-alpha"}
40: grpname[4]={name="Backbone"}
40: grpname[5]={name="MainChain"}
40: grpname[6]={name="MainChain+Cb"}
40: grpname[7]={name="MainChain+H"}
40: grpname[8]={name="SideChain"}
40: grpname[9]={name="SideChain-H"}
40: grpname[10]={name="rest"}
40: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
40: allocated 0 0 0 0 0 0 0 0 0 0
40: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
40: box (3x3):
40: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
40: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
40: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
40: box_rel (3x3):
40: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv (3x3):
40: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev (3x3):
40: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev (3x3):
40: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev (3x3):
40: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: nosehoover_xi: not available
40: x (156x3):
40: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
40: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
40: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
40: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
40: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
40: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
40: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
40: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
40: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
40: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
40: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
40: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
40: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
40: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
40: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
40: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
40: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
40: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
40: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
40: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
40: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
40: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
40: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
40: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
40: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
40: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
40: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
40: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
40: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
40: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
40: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
40: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
40: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
40: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
40: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
40: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
40: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
40: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
40: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
40: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
40: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
40: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
40: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
40: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
40: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
40: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
40: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
40: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
40: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
40: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
40: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
40: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
40: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
40: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
40: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
40: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
40: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
40: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
40: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
40: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
40: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
40: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
40: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
40: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
40: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
40: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
40: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
40: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
40: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
40: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
40: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
40: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
40: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
40: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
40: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
40: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
40: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
40: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
40: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
40: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
40: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
40: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
40: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
40: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
40: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
40: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
40: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
40: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
40: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
40: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
40: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
40: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
40: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
40: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
40: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
40: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
40: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
40: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
40: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
40: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
40: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
40: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
40: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
40: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
40: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
40: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
40: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
40: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
40: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
40: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
40: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
40: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
40: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
40: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
40: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
40: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
40: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
40: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
40: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
40: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
40: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
40: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
40: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
40: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
40: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
40: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
40: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
40: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
40: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
40: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
40: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
40: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
40: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
40: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
40: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
40: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
40: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
40: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
40: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
40: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
40: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
40: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
40: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
40: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
40: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
40: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
40: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
40: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
40: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
40: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
40: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
40: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
40: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
40: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
40: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
40: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
40: v (156x3):
40: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: Group statistics
40: T-Coupling : 156 (total 156 atoms)
40: Energy Mon. : 156 (total 156 atoms)
40: Acceleration: 156 (total 156 atoms)
40: Freeze : 156 (total 156 atoms)
40: User1 : 156 (total 156 atoms)
40: User2 : 156 (total 156 atoms)
40: VCM : 156 (total 156 atoms)
40: Compressed X: 156 (total 156 atoms)
40: Or. Res. Fit: 156 (total 156 atoms)
40: QMMM : 156 (total 156 atoms)
40: [ OK ] DumpTest.WorksWithTpr (46 ms)
40: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
40: [ OK ] DumpTest.WorksWithTprAndMdpWriting (7 ms)
40: [----------] 2 tests from DumpTest (55 ms total)
40:
40: [----------] 4 tests from ReportMethodsTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 1071001524
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectInformation
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
40: [ OK ] ReportMethodsTest.WritesCorrectInformation (4 ms)
40: [ RUN ] ReportMethodsTest.ToolEndToEndTest
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
40: section: Methods
40: subsection: Simulation system
40: A system of 1 molecules (156 atoms) was simulated.
40:
40: subsection: Simulation settings
40: A total of 0 ns were simulated with a time step of 1 fs.
40: Neighbor searching was performed every 10 steps.
40: The Cut-off algorithm was used for electrostatic interactions.
40: with a cut-off of 1 nm.
40: A single cut-off of 1.1 nm was used for Van der Waals interactions.
40: [ OK ] ReportMethodsTest.ToolEndToEndTest (4 ms)
40: [----------] 4 tests from ReportMethodsTest (10 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (100 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (15 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (15 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (14 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (173 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (26 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 18 tests from 4 test cases ran. (7359 ms total)
40: [ PASSED ] 18 tests.
40/52 Test #40: ToolUnitTests ....................... Passed 7.43 sec
test 41
Start 41: FileIOTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 33 tests from 8 test cases.
41: [----------] Global test environment set-up.
41: [----------] 2 tests from FileMD5Test
41: [ RUN ] FileMD5Test.CanComputeMD5
41: [ OK ] FileMD5Test.CanComputeMD5 (6 ms)
41: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
41: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (2 ms)
41: [----------] 2 tests from FileMD5Test (8 ms total)
41:
41: [----------] 3 tests from MrcSerializer
41: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
41: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
41: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
41: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (4 ms)
41: [----------] 3 tests from MrcSerializer (5 ms total)
41:
41: [----------] 4 tests from MrcDensityMap
41: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
41: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms)
41: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
41: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms)
41: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
41: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
41: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
41: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (64 ms)
41: [----------] 4 tests from MrcDensityMap (72 ms total)
41:
41: [----------] 8 tests from MrcDensityMapHeaderTest
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (1 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
41: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.IsSane
41: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
41: [----------] 8 tests from MrcDensityMapHeaderTest (2 ms total)
41:
41: [----------] 9 tests from ReadTest
41: [ RUN ] ReadTest.get_eint_ReadsInteger
41: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
41: [ RUN ] ReadTest.get_eint64_ReadsInteger
41: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsInteger
41: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsFloat
41: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
41: [ RUN ] ReadTest.get_ereal_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not a
41: real value
41:
41:
41: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
41: [----------] 9 tests from ReadTest (1 ms total)
41:
41: [----------] 1 test from FileIOXdrSerializerTest
41: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
41: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (4 ms)
41: [----------] 1 test from FileIOXdrSerializerTest (4 ms total)
41:
41: [----------] 2 tests from TngTest
41: [ RUN ] TngTest.CanOpenTngFile
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: [ OK ] TngTest.CanOpenTngFile (0 ms)
41: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
41: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
41: [----------] 2 tests from TngTest (1 ms total)
41:
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (2 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (10 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms)
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (19 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 33 tests from 8 test cases ran. (112 ms total)
41: [ PASSED ] 33 tests.
41/52 Test #41: FileIOTests ......................... Passed 0.18 sec
test 42
Start 42: SelectionUnitTests
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
42: Test timeout computed to be: 30
42: [==========] Running 192 tests from 11 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from IndexGroupTest
42: [ RUN ] IndexGroupTest.RemovesDuplicates
42: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
42: [----------] 1 test from IndexGroupTest (0 ms total)
42:
42: [----------] 15 tests from IndexBlockTest
42: [ RUN ] IndexBlockTest.CreatesUnknownBlock
42: [ OK ] IndexBlockTest.CreatesUnknownBlock (29 ms)
42: [ RUN ] IndexBlockTest.CreatesAtomBlock
42: [ OK ] IndexBlockTest.CreatesAtomBlock (5 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (3 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (37 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (11 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (15 ms)
42: [ RUN ] IndexBlockTest.CreatesSingleBlock
42: [ OK ] IndexBlockTest.CreatesSingleBlock (2 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
42: [----------] 15 tests from IndexBlockTest (108 ms total)
42:
42: [----------] 11 tests from IndexMapTest
42: [ RUN ] IndexMapTest.InitializesAtomBlock
42: [ OK ] IndexMapTest.InitializesAtomBlock (2 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
42: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
42: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (2 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
42: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (2 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (2 ms)
42: [ RUN ] IndexMapTest.InitializesMoleculeBlock
42: [ OK ] IndexMapTest.InitializesMoleculeBlock (10 ms)
42: [ RUN ] IndexMapTest.MapsSingleBlock
42: [ OK ] IndexMapTest.MapsSingleBlock (9 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocks
42: [ OK ] IndexMapTest.MapsResidueBlocks (2 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
42: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (10 ms)
42: [ RUN ] IndexMapTest.HandlesMultipleRequests
42: [ OK ] IndexMapTest.HandlesMultipleRequests (4 ms)
42: [----------] 11 tests from IndexMapTest (49 ms total)
42:
42: [----------] 3 tests from IndexGroupsAndNamesTest
42: [ RUN ] IndexGroupsAndNamesTest.containsNames
42: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
42: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
42: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms)
42: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
42: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
42: [----------] 3 tests from IndexGroupsAndNamesTest (2 ms total)
42:
42: [----------] 15 tests from NeighborhoodSearchTest
42: [ RUN ] NeighborhoodSearchTest.SimpleSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSearch (68 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
42: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (67 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchBox
42: [ OK ] NeighborhoodSearchTest.GridSearchBox (12 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
42: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (42 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
42: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (20 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
42: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (11 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
42: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (12 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (182 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
42: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
42: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
42: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (16 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
42: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (4 ms)
42: [----------] 15 tests from NeighborhoodSearchTest (440 ms total)
42:
42: [----------] 12 tests from PositionCalculationTest
42: [ RUN ] PositionCalculationTest.ComputesAtomPositions
42: [ OK ] PositionCalculationTest.ComputesAtomPositions (21 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (3 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (9 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionMask
42: [ OK ] PositionCalculationTest.ComputesPositionMask (22 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (21 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (10 ms)
42: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (2 ms)
42: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (2 ms)
42: [----------] 12 tests from PositionCalculationTest (102 ms total)
42:
42: [----------] 29 tests from SelectionCollectionTest
42: [ RUN ] SelectionCollectionTest.HandlesNoSelections
42: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
42: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
42: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
42: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
42: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
42: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
42: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
42: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
42: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
42: [----------] 29 tests from SelectionCollectionTest (60 ms total)
42:
42: [----------] 14 tests from SelectionCollectionInteractiveTest
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
42: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (4 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms)
42: [----------] 14 tests from SelectionCollectionInteractiveTest (43 ms total)
42:
42: [----------] 66 tests from SelectionCollectionDataTest
42: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
42: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
42: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResnr
42: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
42: [ OK ] SelectionCollectionDataTest.HandlesResIndex (14 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
42: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
42: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesChain
42: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMass
42: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCharge
42: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
42: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
42: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
42: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBeta
42: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResname
42: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (26 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
42: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (22 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (9 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
42: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
42: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (14 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
42: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
42: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
42: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
42: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
42: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
42: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
42: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
42: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
42: [----------] 66 tests from SelectionCollectionDataTest (390 ms total)
42:
42: [----------] 17 tests from SelectionOptionTest
42: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
42: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
42: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
42: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
42: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptySelections
42: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
42: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelections
42: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewSelections (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
42: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesAdjuster
42: [ OK ] SelectionOptionTest.HandlesAdjuster (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
42: [----------] 17 tests from SelectionOptionTest (27 ms total)
42:
42: [----------] 9 tests from SelectionFileOptionTest
42: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
42: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (2 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (2 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
42: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
42: [----------] 9 tests from SelectionFileOptionTest (16 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 192 tests from 11 test cases ran. (1241 ms total)
42: [ PASSED ] 192 tests.
42/52 Test #42: SelectionUnitTests .................. Passed 1.39 sec
test 43
Start 43: MdrunTests
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 84 tests from 21 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -1395949561
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.8565400e+03
43: Maximum force = 2.8846870e+03 on atom 3
43: Norm of force = 1.0754448e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (114 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to 1084505019
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.7138666e+04
43: Maximum force = 4.3409717e+03 on atom 2
43: Norm of force = 1.2549793e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (39 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (38 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to 1314111273
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.361 0.181 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.434 16.739
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.462 0.231 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.867 12.852
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (462 ms)
43: [----------] 4 tests from DensityFittingTest (653 ms total)
43:
43: [----------] 3 tests from GromppTest
43: [ RUN ] GromppTest.EmptyMdpFileWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 820831399
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.EmptyMdpFileWorks (24 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1121595466
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group rest: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorks (25 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1508209473
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group Methanol: Single, 3 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 3.0 280.0
43: 6.0- 270.0
43: Simulated annealing for group SOL: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group Methanol is 7.20
43: Number of degrees of freedom in T-Coupling group SOL is 4.80
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (26 ms)
43: [----------] 3 tests from GromppTest (77 ms total)
43:
43: [----------] 1 test from MdrunTest
43: [ RUN ] MdrunTest.WritesHelp
43: [ OK ] MdrunTest.WritesHelp (23 ms)
43: [----------] 1 test from MdrunTest (23 ms total)
43:
43: [----------] 1 test from OriresTest
43: [ RUN ] OriresTest.OriresCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to 1661163607
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 518.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
43: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
43:
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
43: 10 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.522 0.261 199.7
43: (ns/day) (hour/ns)
43: Performance: 7.275 3.299
43: [ OK ] OriresTest.OriresCanRun (1867 ms)
43: [----------] 1 test from OriresTest (1867 ms total)
43:
43: [----------] 3 tests from PmeTest
43: [ RUN ] PmeTest.ReproducesEnergies
43: Setting the LD random seed to 257053828
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.823 0.412 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.405 5.448
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.639 0.320 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.676 4.228
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.762 0.381 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.758 5.044
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (11412 ms)
43: [ RUN ] PmeTest.ScalesTheBox
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 254905779
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.014 0.007 191.9
43: (ns/day) (hour/ns)
43: Performance: 11.798 2.034
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBox (67 ms)
43: [ RUN ] PmeTest.ScalesTheBoxWithWalls
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 423016453
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Searching the wall atom type(s)
43: Number of degrees of freedom in T-Coupling group rest is 13.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: NVE simulation: will use the initial temperature of 966.268 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.050 0.026 197.0
43: (ns/day) (hour/ns)
43: Performance: 3.383 7.094
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBoxWithWalls (31276 ms)
43: [----------] 3 tests from PmeTest (42756 ms total)
43:
43: [----------] 1 test from CompelTest
43: [ RUN ] CompelTest.SwapCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to -707733763
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 1 bonded neighbours molecule type 'NA'
43: Excluding 1 bonded neighbours molecule type 'CL'
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Split0 group 'Ch0' contains 83 atoms.
43: Split1 group 'Ch1' contains 83 atoms.
43: Solvent group 'SOL' contains 11931 atoms.
43: Swap group 'NA+' contains 19 atoms.
43: Swap group 'CL-' contains 19 atoms.
43: Number of degrees of freedom in T-Coupling group System is 27869.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: Removing center of mass motion in the presence of position restraints
43: might cause artifacts. When you are using position restraints to
43: equilibrate a macro-molecule, the artifacts are usually negligible.
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Determining initial numbers of ions per compartment.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 2 steps, 0.0 ps.
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 1 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 5.670 2.835 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.457 52.508
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Copying channel fluxes from checkpoint file data
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 4.975 2.488 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.521 46.073
43: [ OK ] CompelTest.SwapCanRun (10043 ms)
43: [----------] 1 test from CompelTest (10043 ms total)
43:
43: [----------] 6 tests from BondedInteractionsTest
43: [ RUN ] BondedInteractionsTest.NormalBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -616785570
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 186.1
43: (ns/day) (hour/ns)
43: Performance: 51.659 0.465
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalBondWorks (44 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1039599047
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.1
43: (ns/day) (hour/ns)
43: Performance: 52.703 0.455
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedBondWorks (136 ms)
43: [ RUN ] BondedInteractionsTest.NormalAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1280268708
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.0
43: (ns/day) (hour/ns)
43: Performance: 55.083 0.436
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalAngleWorks (35 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1096050821
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.2
43: (ns/day) (hour/ns)
43: Performance: 53.183 0.451
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (49 ms)
43: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 27827711
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.4
43: (ns/day) (hour/ns)
43: Performance: 54.999 0.436
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalDihedralWorks (35 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1330517359
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.7
43: (ns/day) (hour/ns)
43: Performance: 51.593 0.465
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (46 ms)
43: [----------] 6 tests from BondedInteractionsTest (345 ms total)
43:
43: [----------] 6 tests from MdrunTerminationTest
43: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
43: Setting the LD random seed to -1694040690
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.388 0.194 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.335 17.975
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.528 0.264 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.982 24.445
43: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (508 ms)
43: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
43: Setting the LD random seed to 750960112
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 1, rlist from 1.024 to 1
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 100 steps, 0.1 ps.
43:
43: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.394 0.197 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.316 18.244
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 102
43: Writing statusfile with starting step 0 and length 102 steps...
43: time 0.000 and length 0.102 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.329 0.165 199.7
43: (ns/day) (hour/ns)
43: Performance: 53.042 0.452
43: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (411 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
43: Setting the LD random seed to -638799146
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.416 0.208 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.244 19.287
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.462 0.231 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.122 21.391
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 6
43: Writing statusfile with starting step 0 and length 6 steps...
43: time 0.000 and length 0.006 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.431 0.216 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.202 19.973
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 8
43: Writing statusfile with starting step 0 and length 8 steps...
43: time 0.000 and length 0.008 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.372 0.186 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.394 17.217
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.001 0.001 169.4
43: (ns/day) (hour/ns)
43: Performance: 111.230 0.216
43: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (938 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
43: Setting the LD random seed to -1878359787
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.452 0.226 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.146 20.946
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.439 0.220 199.6
43: (ns/day) (hour/ns)
43: Performance: 1.966 12.205
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (496 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
43: Setting the LD random seed to 230367130
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.327 0.164 199.5
43: (ns/day) (hour/ns)
43: Performance: 1.583 15.159
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (203 ms)
43: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
43: Setting the LD random seed to 44248178
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.341 0.171 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.519 15.799
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.417 0.209 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.243 19.313
43: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (429 ms)
43: [----------] 6 tests from MdrunTerminationTest (2986 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -2010600426
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.001 184.5
43: (ns/day) (hour/ns)
43: Performance: 61.904 0.388
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (35 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -340623163
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 183.7
43: (ns/day) (hour/ns)
43: Performance: 64.528 0.372
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (36 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -604867682
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 183.5
43: (ns/day) (hour/ns)
43: Performance: 64.805 0.370
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (36 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -841324137
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.007 0.003 192.7
43: (ns/day) (hour/ns)
43: Performance: 24.760 0.969
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (195 ms)
43: [----------] 4 tests from MimicTest (302 ms total)
43:
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
43: Setting the LD random seed to -2032714112
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.439 0.220 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.785 30.555
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (270 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
43: Setting the LD random seed to 996233922
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.928 1.464 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.118 203.359
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (1511 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
43: Setting the LD random seed to 662572757
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.726 0.363 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.475 50.477
43:
Reading frame 0 time 0.000
43: # Atoms 3
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (405 ms)
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (2187 ms total)
43:
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.525 0.263 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.595 4.290
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.425 0.213 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.655 6.566
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.490 0.245 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.169 7.574
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (803 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.535 0.268 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.487 4.374
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.464 0.232 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.346 7.172
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.576 0.288 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.700 8.888
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (878 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.554 0.277 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.293 4.534
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.775 0.388 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.004 11.975
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.598 0.299 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.600 9.232
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1054 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.646 0.323 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.547 5.278
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.730 0.365 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.128 11.280
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.220 0.610 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.274 18.835
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1389 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.528 0.764 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.922 12.489
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.975 0.988 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.787 30.490
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.778 0.389 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.997 12.019
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (2232 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.874 0.437 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.361 7.141
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.691 0.346 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.250 10.668
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.753 0.377 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.064 11.626
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1247 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.723 0.362 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.058 5.914
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.416 0.208 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.732 6.430
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.505 0.253 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.076 7.802
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (922 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.081 0.541 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.717 8.833
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.616 0.309 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.520 9.525
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.617 0.309 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.518 9.532
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1255 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.668 0.335 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.391 5.466
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.524 0.262 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.963 8.100
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.678 0.339 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.293 10.468
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (1267 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.572 0.286 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.131 4.677
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.524 0.262 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.964 8.098
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.744 0.373 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.087 11.498
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1189 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.636 0.318 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.613 5.203
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.941 0.471 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.650 14.542
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.982 0.492 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.582 15.172
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1722 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.143 0.572 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.567 9.349
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.559 0.280 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.779 8.636
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.644 0.322 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.413 9.945
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1555 ms)
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (15517 ms total)
43:
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.688 0.345 199.7
43: (ns/day) (hour/ns)
43: Performance: 4.263 5.630
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.703 0.352 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.206 10.879
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.791 0.396 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.964 12.221
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1365 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.547 0.774 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.899 12.640
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.727 0.364 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.137 11.232
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.834 0.417 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.864 12.879
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1801 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.823 0.412 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.565 6.732
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.741 0.371 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.093 11.465
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.229 1.115 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.698 34.408
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (2355 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.007 0.504 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.913 8.238
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.768 0.385 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.020 11.881
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.641 0.321 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.422 9.909
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1605 ms)
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (7126 ms total)
43:
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.585 0.293 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.020 4.781
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.441 0.221 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.521 6.815
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.574 0.287 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.707 8.866
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (894 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.465 0.233 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.316 3.800
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.507 0.254 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.060 7.842
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.574 0.287 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.707 8.866
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (866 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.447 0.224 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.569 3.654
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.512 0.257 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.030 7.920
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.513 0.257 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.032 7.917
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (820 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.630 0.815 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.802 13.322
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.646 0.323 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.406 9.975
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.490 0.245 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.172 7.567
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1467 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.557 0.278 199.9
43: (ns/day) (hour/ns)
43: Performance: 5.275 4.550
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.019 0.510 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.525 15.735
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.686 0.343 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.265 10.595
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (1223 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.798 0.399 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.680 6.522
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.841 0.421 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.848 12.988
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.544 0.272 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.855 8.408
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1189 ms)
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (6461 ms total)
43:
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.056 0.528 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.780 8.634
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.471 0.736 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.057 22.715
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.797 0.399 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.951 12.300
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1755 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.686 0.343 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.279 5.609
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 6.246 3.124 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.249 96.408
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.192 0.597 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.304 18.411
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (4156 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.885 0.443 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.316 7.238
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.620 0.310 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.506 9.578
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.797 0.399 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.951 12.303
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1244 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.776 0.388 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.784 6.343
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.563 0.282 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.758 8.700
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.409 0.705 200.0
43: (ns/day) (hour/ns)
43: Performance: 1.103 21.755
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1466 ms)
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (8621 ms total)
43:
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.138 0.569 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.579 9.305
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.464 0.232 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.347 7.170
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.374 0.187 199.7
43: (ns/day) (hour/ns)
43: Performance: 4.157 5.773
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1079 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.463 0.232 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.340 3.786
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.374 0.187 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.150 5.784
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.907 0.954 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.815 29.438
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1467 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.685 0.343 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.286 5.600
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.440 0.221 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.523 6.812
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.441 0.221 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.522 6.814
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (877 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.864 0.432 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.399 7.060
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.529 0.265 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.933 8.183
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.574 0.287 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.707 8.865
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1077 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.484 0.242 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.068 3.955
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.818 0.410 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.898 12.645
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.441 0.221 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.522 6.814
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (967 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.596 0.298 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.926 4.873
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.485 0.243 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.200 7.501
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.641 0.321 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.425 9.898
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (955 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.529 0.265 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.543 4.330
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.574 0.287 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.705 8.873
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.507 0.254 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.065 7.830
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (899 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.573 0.287 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.120 4.688
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.441 0.221 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.523 6.812
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.618 0.309 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.514 9.546
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (910 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.732 0.366 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.013 5.981
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.553 0.277 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.811 8.538
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.486 0.743 200.0
43: (ns/day) (hour/ns)
43: Performance: 1.046 22.938
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1478 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (9714 ms total)
43:
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
43: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.460 0.730 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.011 11.934
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.604 0.302 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.571 9.333
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.491 0.246 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.166 7.580
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1429 ms)
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (1430 ms total)
43:
43: [----------] 3 tests from Checking/InitialConstraintsTest
43: [ RUN ] Checking/InitialConstraintsTest.Works/0
43: Setting the LD random seed to 1905705896
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.203 0.602 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.287 83.572
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (640 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/1
43: Setting the LD random seed to -129549044
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.986 0.493 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.351 68.470
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (534 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: Integrator method md-vv-avek is implemented primarily for validation
43: purposes; for molecular dynamics, you should probably be using md or md-vv
43:
43: Setting the LD random seed to -1461656555
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.404 0.202 199.7
43: (ns/day) (hour/ns)
43: Performance: 0.854 28.109
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (244 ms)
43: [----------] 3 tests from Checking/InitialConstraintsTest (1419 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to 1712338782
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 49569.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.636 0.318 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.628 14.740
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1432 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to -1144701467
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 52293.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.1977063e+03
43: Maximum force = 1.7794877e+04 on atom 9
43: Norm of force = 7.8732901e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (1042 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (2475 ms total)
43:
43: [----------] 2 tests from Argon12/OutputFiles
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.126 0.563 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.608 9.202
43: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (603 ms)
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.810 0.405 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.623 6.624
43: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (446 ms)
43: [----------] 2 tests from Argon12/OutputFiles (1049 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/Trajectories
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
43: Setting the LD random seed to -581045584
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.460 0.230 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.625 9.144
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (276 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
43: Setting the LD random seed to -1815266363
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.575 0.288 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.103 11.413
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (333 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
43: Setting the LD random seed to -859282912
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.686 0.343 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.762 13.622
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (388 ms)
43: [----------] 3 tests from MdrunCanWrite/Trajectories (998 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
43: Setting the LD random seed to -1270550285
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.933 0.467 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.555 43.205
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (510 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
43: Setting the LD random seed to -377958486
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.568 0.284 199.7
43: (ns/day) (hour/ns)
43: Performance: 0.912 26.313
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (328 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
43: Setting the LD random seed to 880229057
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.543 0.272 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.953 25.182
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (315 ms)
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories (1155 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 84 tests from 21 test cases ran. (117211 ms total)
43: [ PASSED ] 84 tests.
43:
43: YOU HAVE 12 DISABLED TESTS
43:
43/52 Test #43: MdrunTests .......................... Passed 117.31 sec
test 44
Start 44: MdrunNonIntegratorTests
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 58 tests from 5 test cases.
44: [----------] Global test environment set-up.
44: [----------] 1 test from NonbondedBenchTest
44: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
44: System size: 3000 atoms
44: Cut-off radius: 1 nm
44: Number of threads: 1
44: Number of iterations: 1
44: Compute energies: no
44: Ewald excl. corr.: analytical
44:
44: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
44: total useful
44: Ewald all geom. no 0.000 0.0000 inf inf
44: [ OK ] NonbondedBenchTest.BasicEndToEndTest (527 ms)
44: [----------] 1 test from NonbondedBenchTest (528 ms total)
44:
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -4.7990990e+01
44: Maximum force = 1.8629828e+02 on atom 13
44: Norm of force = 8.7721844e+01
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (3206 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 3.02331e+02 on atom 3
44: F-Norm = 1.18024e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -5.5862099e+01
44: Maximum force = 4.2728845e+02 on atom 13
44: Norm of force = 1.8453478e+02
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (3417 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.1937714e+02
44: Maximum force = 9.9988643e+03 on atom 9
44: Norm of force = 4.6166996e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1038 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44:
44: NOTE 3 [file glycine_vacuo.top, line 12]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41575e+04 on atom 10
44: F-Norm = 1.18451e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.5174377e+02
44: Maximum force = 7.4208838e+03 on atom 9
44: Norm of force = 3.5693005e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1159 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.5698413e+02
44: Maximum force = 4.5704984e+02 on atom 17
44: Norm of force = 1.8327747e+02
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (147 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44:
44: NOTE 4 [file unknown]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 1.06801e+03 on atom 28
44: F-Norm = 4.26916e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.6941180e+02
44: Maximum force = 2.1832491e+02 on atom 17
44: Norm of force = 7.9220732e+01
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (145 ms)
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (9116 ms total)
44:
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents converged to Fmax < 10 in 1 steps
44: Potential Energy = -9.7425699e-01
44: Maximum force = 4.0132303e+00 on atom 1
44: Norm of force = 1.6383944e+00
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (49 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.9064207e-01
44: Maximum force = 2.5781622e+00 on atom 1
44: Norm of force = 1.0525302e+00
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (51 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.9064207e-01
44: Maximum force = 2.5781622e+00 on atom 1
44: Norm of force = 1.0525302e+00
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (52 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.1939697e+02
44: Maximum force = 9.9704248e+03 on atom 9
44: Norm of force = 4.6227540e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1200 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.5625757e+02
44: Maximum force = 7.5018242e+03 on atom 9
44: Norm of force = 3.6139019e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1102 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 5.6111725e+02
44: Maximum force = 1.2685491e+04 on atom 10
44: Norm of force = 6.0643622e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1108 ms)
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3566 ms total)
44:
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.809 0.405 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.629 6.614
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
44:
44: trr version: GMX_trn_file (single precision)
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.3
44: (ns/day) (hour/ns)
44: Performance: 357.384 0.067
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (476 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.519 0.260 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.658 4.242
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.7
44: (ns/day) (hour/ns)
44: Performance: 495.503 0.048
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (324 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.538 0.269 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.452 4.402
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.1
44: (ns/day) (hour/ns)
44: Performance: 490.259 0.049
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (333 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.618 0.309 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.748 5.055
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.5
44: (ns/day) (hour/ns)
44: Performance: 484.133 0.050
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (365 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.704 0.353 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.167 5.760
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.009 0.005 192.8
44: (ns/day) (hour/ns)
44: Performance: 323.187 0.074
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (3719 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.695 0.348 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.225 5.680
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.007 0.004 192.5
44: (ns/day) (hour/ns)
44: Performance: 404.053 0.059
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (3803 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.612 0.306 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.793 5.007
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.007 0.004 189.9
44: (ns/day) (hour/ns)
44: Performance: 376.403 0.064
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (3763 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.617 0.309 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.756 5.046
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.9
44: (ns/day) (hour/ns)
44: Performance: 442.127 0.054
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (3542 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.673 0.337 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.361 5.504
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.011 0.005 194.0
44: (ns/day) (hour/ns)
44: Performance: 269.693 0.089
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (484 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.615 0.308 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.773 5.028
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.011 0.005 194.3
44: (ns/day) (hour/ns)
44: Performance: 267.178 0.090
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (455 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.679 0.340 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.322 5.553
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.011 0.006 194.2
44: (ns/day) (hour/ns)
44: Performance: 257.690 0.093
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (603 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.559 0.280 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.251 4.571
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.011 0.006 194.3
44: (ns/day) (hour/ns)
44: Performance: 265.097 0.091
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (502 ms)
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (18371 ms total)
44:
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.730 0.365 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.021 5.969
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 202.020 0.119
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (511 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.773 0.387 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.797 6.321
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 200.130 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (535 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.862 0.431 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.405 7.048
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 189.3
44: (ns/day) (hour/ns)
44: Performance: 160.927 0.149
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (583 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.877 0.439 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.347 7.171
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.9
44: (ns/day) (hour/ns)
44: Performance: 187.754 0.128
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (601 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.718 0.359 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.088 5.871
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.8
44: (ns/day) (hour/ns)
44: Performance: 186.301 0.129
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (523 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.741 0.371 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.961 6.060
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 188.0
44: (ns/day) (hour/ns)
44: Performance: 185.902 0.129
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (532 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.495 0.248 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.927 4.049
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 188.1
44: (ns/day) (hour/ns)
44: Performance: 184.620 0.130
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (410 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.744 0.372 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.946 6.083
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.3
44: (ns/day) (hour/ns)
44: Performance: 187.668 0.128
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (527 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.698 0.349 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.206 5.707
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 188.0
44: (ns/day) (hour/ns)
44: Performance: 183.073 0.131
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (503 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.693 0.347 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.234 5.668
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 188.1
44: (ns/day) (hour/ns)
44: Performance: 183.750 0.131
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (499 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.752 0.376 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.904 6.148
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.7
44: (ns/day) (hour/ns)
44: Performance: 203.099 0.118
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (528 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.730 0.365 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.020 5.971
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.8
44: (ns/day) (hour/ns)
44: Performance: 201.221 0.119
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (512 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.728 0.364 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.034 5.950
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 200.182 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (511 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.972 0.486 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.022 7.941
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.6
44: (ns/day) (hour/ns)
44: Performance: 202.558 0.118
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (634 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.772 0.386 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.801 6.314
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 199.883 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (533 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.706 0.353 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.161 5.767
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.8
44: (ns/day) (hour/ns)
44: Performance: 201.018 0.119
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (500 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.749 0.375 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.918 6.126
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.8
44: (ns/day) (hour/ns)
44: Performance: 199.844 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (522 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.460 0.730 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.012 11.931
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.0
44: (ns/day) (hour/ns)
44: Performance: 199.702 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (878 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 6.355 3.178 200.0
44: (ns/day) (hour/ns)
44: Performance: 0.462 51.921
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 201.294 0.119
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (3326 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.986 0.493 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.977 8.061
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 188.1
44: (ns/day) (hour/ns)
44: Performance: 202.785 0.118
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (640 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.905 0.453 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.246 7.394
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.3
44: (ns/day) (hour/ns)
44: Performance: 200.312 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (601 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.837 0.418 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.510 6.838
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 188.2
44: (ns/day) (hour/ns)
44: Performance: 202.925 0.118
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (566 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.264 0.632 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.323 10.332
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.8
44: (ns/day) (hour/ns)
44: Performance: 198.799 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (864 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.559 0.780 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.884 12.740
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.0
44: (ns/day) (hour/ns)
44: Performance: 198.013 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (1011 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.136 0.569 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.584 9.289
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.3
44: (ns/day) (hour/ns)
44: Performance: 198.626 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (800 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.225 0.613 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.396 10.017
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 188.3
44: (ns/day) (hour/ns)
44: Performance: 199.844 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (844 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.824 0.413 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.560 6.743
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 197.556 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (645 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.914 0.457 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.212 7.471
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 199.295 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (689 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.912 0.457 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.217 7.461
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.0
44: (ns/day) (hour/ns)
44: Performance: 197.924 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (689 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.911 0.456 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.221 7.452
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.8
44: (ns/day) (hour/ns)
44: Performance: 196.786 0.122
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (689 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 2.179 1.090 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.347 17.811
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 199.566 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (1322 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.421 0.711 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.065 11.620
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.0
44: (ns/day) (hour/ns)
44: Performance: 199.088 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (944 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 2.132 1.067 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.377 17.428
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.008 185.1
44: (ns/day) (hour/ns)
44: Performance: 193.292 0.124
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (1303 ms)
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (24779 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 58 tests from 5 test cases ran. (56361 ms total)
44: [ PASSED ] 58 tests.
44/52 Test #44: MdrunNonIntegratorTests ............. Passed 56.45 sec
test 45
Start 45: MdrunTpiTests
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 2 tests from 1 test case.
45: [----------] Global test environment set-up.
45: [----------] 2 tests from Simple/TpiTest
45: [ RUN ] Simple/TpiTest.ReproducesOutput/0
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 1 OpenMP thread
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/0 (3565 ms)
45: [ RUN ] Simple/TpiTest.ReproducesOutput/1
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 1 OpenMP thread
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/1 (3591 ms)
45: [----------] 2 tests from Simple/TpiTest (7157 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 2 tests from 1 test case ran. (7158 ms total)
45: [ PASSED ] 2 tests.
45/52 Test #45: MdrunTpiTests ....................... Passed 7.23 sec
test 46
Start 46: MdrunMpiTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 22 tests from 7 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from DomainDecompositionSpecialCasesTest
46: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -1029497301
46: Generated 3 of the 3 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 3 of the 3 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 9.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.006 0.002 316.2
46: (ns/day) (hour/ns)
46: Performance: 47.805 0.502
46: This run will generate roughly 0 Mb of data
46: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (84 ms)
46: [----------] 1 test from DomainDecompositionSpecialCasesTest (85 ms total)
46:
46: [----------] 4 tests from MimicTest
46: [ RUN ] MimicTest.OneQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 821301308
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.560 0.672 380.7
46: (ns/day) (hour/ns)
46: Performance: 0.128 186.797
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.OneQuantumMol (2082 ms)
46: [ RUN ] MimicTest.AllQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 1686535771
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.520 0.660 381.8
46: (ns/day) (hour/ns)
46: Performance: 0.131 183.325
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.AllQuantumMol (2050 ms)
46: [ RUN ] MimicTest.TwoQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 1715642215
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.560 0.670 382.1
46: (ns/day) (hour/ns)
46: Performance: 0.129 186.100
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.TwoQuantumMol (2275 ms)
46: [ RUN ] MimicTest.BondCuts
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -73494898
46: Generated 2211 of the 2211 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2211 of the 2211 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
46: Number of degrees of freedom in T-Coupling group rest is 66.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: NVE simulation: will use the initial temperature of 300.368 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
46:
46: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.489 0.652 381.6
46: (ns/day) (hour/ns)
46: Performance: 0.132 181.166
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
46: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.BondCuts (2116 ms)
46: [----------] 4 tests from MimicTest (8527 ms total)
46:
46: [----------] 1 test from MultiSimTerminationTest
46: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
46: [----------] 1 test from MultiSimTerminationTest (0 ms total)
46:
46: [----------] 3 tests from PmeTest
46: [ RUN ] PmeTest.ReproducesEnergies
46: Setting the LD random seed to -1481833224
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 9.257 2.355 393.2
46: (ns/day) (hour/ns)
46: Performance: 0.771 31.145
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 8.453 2.152 392.8
46: (ns/day) (hour/ns)
46: Performance: 0.843 28.469
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 7.987 2.035 392.5
46: (ns/day) (hour/ns)
46: Performance: 0.892 26.914
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (30228 ms)
46: [ RUN ] PmeTest.ScalesTheBox
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -2078045829
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.440 0.150 294.0
46: (ns/day) (hour/ns)
46: Performance: 0.577 41.607
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBox (1082 ms)
46: [ RUN ] PmeTest.ScalesTheBoxWithWalls
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 2015792805
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Searching the wall atom type(s)
46: Number of degrees of freedom in T-Coupling group rest is 13.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: NVE simulation: will use the initial temperature of 966.268 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.575 0.185 311.0
46: (ns/day) (hour/ns)
46: Performance: 0.468 51.334
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBoxWithWalls (63532 ms)
46: [----------] 3 tests from PmeTest (94842 ms total)
46:
46: [----------] 1 test from ReplicaExchangeTerminationTest
46: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (1 ms)
46: [----------] 1 test from ReplicaExchangeTerminationTest (1 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.7991020e+01
46: Maximum force = 1.8629866e+02 on atom 13
46: Norm of force = 8.7722033e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (6288 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.5862247e+01
46: Maximum force = 4.2727914e+02 on atom 13
46: Norm of force = 1.8453180e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (7861 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1937704e+02
46: Maximum force = 9.9988633e+03 on atom 9
46: Norm of force = 4.6166993e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4190 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5174442e+02
46: Maximum force = 7.4208892e+03 on atom 9
46: Norm of force = 3.5693002e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5758 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.5698419e+02
46: Maximum force = 4.5704996e+02 on atom 17
46: Norm of force = 1.8327748e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (5287 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06801e+03 on atom 28
46: F-Norm = 4.26916e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.6941193e+02
46: Maximum force = 2.1835349e+02 on atom 17
46: Norm of force = 7.9216550e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7073 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (36457 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.7425699e-01
46: Maximum force = 4.0132303e+00 on atom 3
46: Norm of force = 1.6383944e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1629 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 3
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 3
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2157 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1939685e+02
46: Maximum force = 9.9704248e+03 on atom 9
46: Norm of force = 4.6227568e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3863 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5625764e+02
46: Maximum force = 7.5018237e+03 on atom 9
46: Norm of force = 3.6139019e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5383 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1007 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (14062 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 22 tests from 7 test cases ran. (153978 ms total)
46: [ PASSED ] 22 tests.
46:
46: YOU HAVE 4 DISABLED TESTS
46:
46/52 Test #46: MdrunMpiTests ....................... Passed 154.06 sec
test 47
Start 47: MdrunMpiCoordinationTestsOneRank
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
47: Test timeout computed to be: 480
47: [==========] Running 27 tests from 3 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest
47: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.394 0.395 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.722 6.448
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.332 0.333 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.415 5.436
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.352 0.352 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.168 5.758
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.325 0.325 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.519 5.311
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.391 0.391 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.756 6.390
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.350 0.351 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.188 5.730
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2611 ms)
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest (2611 ms total)
47:
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.392 0.393 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.741 6.415
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.399 0.399 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.678 6.526
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.532 0.532 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.761 8.694
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.282 0.283 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.193 4.622
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.282 0.283 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.196 4.619
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.204 0.204 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.191 3.337
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2611 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.259 0.259 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.662 4.239
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.355 0.355 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.136 5.803
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.347 0.348 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.221 5.686
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.402 0.403 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.648 6.579
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.216 0.216 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.795 3.532
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.305 0.305 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.815 4.985
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2366 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.558 0.559 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.630 9.127
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.299 0.299 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.906 4.892
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.326 0.326 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.500 5.334
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.259 0.259 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.666 4.236
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.321 0.322 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.565 5.257
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.325 0.326 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.507 5.325
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2521 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.425 0.425 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.455 6.947
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.421 0.422 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.483 6.890
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.753 0.753 99.9
47: (ns/day) (hour/ns)
47: Performance: 1.950 12.308
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.384 0.384 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.823 6.277
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.075 1.075 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.366 17.566
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.984 0.984 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.493 16.078
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (4588 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.481 0.481 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.054 7.859
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.650 0.650 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.260 10.621
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 2.345 2.346 100.0
47: (ns/day) (hour/ns)
47: Performance: 0.626 38.333
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.595 0.596 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.465 9.737
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.341 0.342 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.298 5.584
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.302 0.303 99.7
47: (ns/day) (hour/ns)
47: Performance: 4.854 4.944
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (5158 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.289 0.290 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.070 4.734
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.387 0.388 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.788 6.336
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.294 0.295 99.7
47: (ns/day) (hour/ns)
47: Performance: 4.987 4.813
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.412 0.413 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.558 6.746
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.271 0.272 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.401 4.444
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.337 0.338 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.348 5.519
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2754 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.368 0.368 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.989 6.017
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.907 0.907 99.9
47: (ns/day) (hour/ns)
47: Performance: 1.619 14.828
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.253 0.254 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.794 4.142
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.337 0.338 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.350 5.517
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.702 0.703 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.091 11.479
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.305 0.305 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.813 4.987
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3319 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.273 0.273 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.373 4.467
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.280 0.280 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.244 4.576
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.502 0.503 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.922 8.213
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.680 0.681 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.157 11.125
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.302 0.303 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.847 4.952
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.324 0.325 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.519 5.311
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2923 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.513 0.513 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.861 8.390
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.365 0.366 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.016 5.976
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.580 0.580 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.531 9.481
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.506 0.507 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.900 8.277
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.374 0.375 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.921 6.121
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.422 0.423 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.475 6.906
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3154 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.625 0.625 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.349 10.217
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.692 0.692 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.122 11.308
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.343 0.343 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.279 5.608
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.331 0.332 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.427 5.421
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.298 0.299 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.921 4.878
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.300 0.301 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.885 4.913
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (3034 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.325 0.325 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.514 5.316
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.321 0.321 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.573 5.249
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.284 0.285 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.157 4.654
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.308 0.308 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.764 5.038
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.295 0.296 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.969 4.830
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.332 0.332 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.421 5.429
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2145 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.313 0.314 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.685 5.123
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.332 0.333 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.416 5.434
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.257 0.258 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.696 4.214
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.321 0.322 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.561 5.262
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.357 0.358 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.108 5.842
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.318 0.318 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.613 5.203
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2211 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.336 0.336 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.366 5.497
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.366 0.366 100.0
47: (ns/day) (hour/ns)
47: Performance: 4.011 5.984
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.328 0.328 100.0
47: (ns/day) (hour/ns)
47: Performance: 4.475 5.363
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.428 0.428 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.431 6.996
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.386 0.386 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.808 6.302
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.282 0.282 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.213 4.604
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2455 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.492 0.492 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.985 8.039
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.843 0.843 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.742 13.778
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.312 0.313 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.700 5.107
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.323 0.323 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.541 5.285
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.678 0.679 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.163 11.094
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.256 0.257 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.724 4.193
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (3766 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.303 0.303 100.0
47: (ns/day) (hour/ns)
47: Performance: 4.841 4.957
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.322 0.322 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.565 5.257
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.314 0.314 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.682 5.125
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.291 0.291 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.051 4.752
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.920 0.920 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.596 15.039
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.277 0.278 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.291 4.536
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (3033 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 2.839 2.839 100.0
47: (ns/day) (hour/ns)
47: Performance: 0.517 46.393
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.343 0.343 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.278 5.610
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.267 0.268 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.488 4.373
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.320 0.320 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.586 5.233
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.270 0.271 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.426 4.423
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.325 0.326 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.509 5.323
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (4820 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.361 0.361 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.066 5.903
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.346 0.347 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.236 5.666
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.271 0.272 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.403 4.442
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.271 0.271 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.413 4.434
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.271 0.271 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.412 4.434
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.260 0.260 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.645 4.251
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (2300 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.414 0.414 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.545 6.770
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.432 0.432 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.397 7.066
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.314 0.315 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.664 5.145
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.287 0.288 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.107 4.700
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.376 0.376 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.901 6.151
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.420 0.421 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.490 6.878
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (2667 ms)
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (55834 ms total)
47:
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.465 1.466 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.002 23.946
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.347 0.348 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.227 5.678
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.571 0.571 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.572 9.333
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.504 0.505 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.911 8.245
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.488 0.489 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.004 7.989
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.928 0.928 99.9
47: (ns/day) (hour/ns)
47: Performance: 1.582 15.167
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (23715 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.344 0.344 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.271 5.620
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.254 0.255 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.765 4.163
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.328 0.328 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.474 5.364
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.372 0.372 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.945 6.084
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.379 0.380 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.865 6.210
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.423 0.424 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.464 6.928
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (21998 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.324 0.324 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.536 5.291
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.526 0.526 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.791 8.600
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.243 0.244 99.7
47: (ns/day) (hour/ns)
47: Performance: 6.026 3.983
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.321 0.322 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.563 5.260
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.315 0.316 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.652 5.159
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.409 0.410 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.584 6.697
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (21507 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.455 0.455 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.227 7.437
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.334 0.334 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.396 5.460
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.397 0.398 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.692 6.500
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.297 0.298 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.931 4.867
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.383 0.383 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.835 6.259
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.344 0.344 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.264 5.628
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (21457 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.307 0.307 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.783 5.018
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.299 0.299 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.912 4.886
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.603 0.603 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.434 9.860
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.537 0.537 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.733 8.780
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.523 0.523 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.806 8.554
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.578 0.578 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.539 9.452
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (22098 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.398 0.398 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.689 6.505
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.401 0.402 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.658 6.561
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.590 0.591 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.486 9.656
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.958 0.958 99.9
47: (ns/day) (hour/ns)
47: Performance: 1.533 15.661
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.371 0.371 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.958 6.063
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.431 0.432 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.403 7.053
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (22390 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.481 0.481 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.055 7.856
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.383 0.383 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.835 6.258
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.314 0.314 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.675 5.133
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.418 0.418 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.512 6.834
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.307 0.308 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.776 5.025
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.312 0.312 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.701 5.105
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (21438 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.372 0.372 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.948 6.079
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.336 0.337 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.363 5.501
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.426 0.427 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.444 6.969
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.487 0.487 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.015 7.960
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.310 0.310 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.732 5.071
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.566 0.566 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.593 9.256
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (21714 ms)
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (176322 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 27 tests from 3 test cases ran. (234767 ms total)
47: [ PASSED ] 27 tests.
47/52 Test #47: MdrunMpiCoordinationTestsOneRank .... Passed 234.85 sec
test 48
Start 48: MdrunMpiCoordinationTestsTwoRanks
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
48: Test timeout computed to be: 480
48: [==========] Running 27 tests from 3 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest
48: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.772 0.386 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.801 6.314
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.695 0.348 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.219 5.688
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.686 0.344 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.274 5.616
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.644 0.323 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.550 5.275
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.642 0.321 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.572 5.250
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.716 0.359 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.095 5.861
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2627 ms)
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest (2627 ms total)
48:
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.703 0.352 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.172 5.752
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.926 0.463 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.170 7.570
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.956 0.479 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.069 7.820
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.794 0.398 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.694 6.497
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.707 0.354 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.145 5.790
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.001 0.501 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.931 8.189
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2978 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.135 0.568 199.9
48: (ns/day) (hour/ns)
48: Performance: 2.587 9.276
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.765 0.383 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.833 6.261
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.679 0.340 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.319 5.556
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.949 0.475 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.092 7.762
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.397 0.699 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.101 11.422
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.318 1.159 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.267 18.946
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4076 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.280 1.140 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.288 18.634
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.553 0.277 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.303 4.526
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 5.708 2.855 199.9
48: (ns/day) (hour/ns)
48: Performance: 0.515 46.646
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.730 0.366 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.016 5.977
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.188 0.595 199.7
48: (ns/day) (hour/ns)
48: Performance: 2.470 9.716
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.589 0.296 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.971 4.828
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (5890 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.722 0.361 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.064 5.906
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.708 0.355 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.143 5.793
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.051 0.526 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.792 8.595
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.019 0.510 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.878 8.339
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.841 0.421 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.486 6.884
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.586 0.293 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.006 4.794
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3044 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.613 0.307 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.788 5.013
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.685 0.343 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.283 5.604
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.716 0.358 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.097 5.858
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.574 0.288 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.105 4.702
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.730 0.366 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.017 5.974
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.582 0.292 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.038 4.764
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2389 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.723 0.862 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.704 14.085
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.307 0.654 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.245 10.689
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.726 0.864 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.701 14.110
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.818 1.410 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.042 23.040
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.758 1.380 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.064 22.553
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.755 0.378 199.5
48: (ns/day) (hour/ns)
48: Performance: 3.882 6.183
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (6457 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.736 0.368 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.987 6.019
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.699 0.350 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.196 5.720
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.641 0.321 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.569 5.253
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.753 0.377 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.896 6.160
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.864 0.432 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.397 7.065
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.703 0.352 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.169 5.757
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2600 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.582 0.291 199.8
48: (ns/day) (hour/ns)
48: Performance: 5.041 4.761
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.633 0.317 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.637 5.176
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.624 0.313 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.698 5.109
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.287 0.644 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.280 10.525
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.370 0.685 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.143 11.201
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.657 0.329 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.461 5.381
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3099 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.832 0.416 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.529 6.800
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.662 0.332 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.426 5.422
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.663 0.333 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.416 5.434
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.551 0.277 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.312 4.518
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.654 0.328 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.477 5.361
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.616 0.309 199.3
48: (ns/day) (hour/ns)
48: Performance: 4.754 5.049
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2311 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.583 0.292 199.8
48: (ns/day) (hour/ns)
48: Performance: 5.034 4.768
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.567 0.284 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.170 4.642
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.568 0.287 197.7
48: (ns/day) (hour/ns)
48: Performance: 5.111 4.696
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.831 0.416 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.527 6.804
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.726 0.364 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.035 5.948
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.756 0.381 198.2
48: (ns/day) (hour/ns)
48: Performance: 3.851 6.233
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2406 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.805 0.403 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.645 6.584
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.706 0.353 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.158 5.771
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.551 0.276 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.322 4.510
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.593 0.297 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.940 4.858
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.571 0.286 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.131 4.677
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.638 0.319 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.599 5.218
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2358 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.745 0.373 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.939 6.093
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.211 1.106 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.328 18.074
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.603 0.803 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.830 13.113
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.170 1.086 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.353 17.744
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.616 0.309 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.756 5.046
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 7.362 3.682 200.0
48: (ns/day) (hour/ns)
48: Performance: 0.399 60.160
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (8148 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.671 0.336 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.367 5.495
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.686 0.344 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.273 5.617
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.591 0.296 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.957 4.841
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.520 0.261 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.630 4.263
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.564 0.283 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.194 4.621
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.653 0.327 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.488 5.347
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2296 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.805 0.403 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.647 6.581
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.693 0.347 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.234 5.668
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.828 0.415 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.541 6.777
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.895 0.948 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.549 15.493
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.893 0.447 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.283 7.311
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.937 0.469 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.131 7.664
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (3546 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.916 0.459 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.202 7.496
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.790 0.896 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.640 14.635
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.892 0.447 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.287 7.301
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.669 0.336 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.377 5.483
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.735 0.368 199.5
48: (ns/day) (hour/ns)
48: Performance: 3.990 6.015
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.794 0.398 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.690 6.504
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (3333 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.775 0.388 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.787 6.337
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.796 0.398 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.686 6.511
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.926 0.464 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.167 7.577
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.522 0.762 199.7
48: (ns/day) (hour/ns)
48: Performance: 1.927 12.453
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.700 0.351 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.188 5.731
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.577 0.289 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.078 4.726
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (3132 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.588 0.294 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.991 4.808
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.596 0.298 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.925 4.873
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.796 0.399 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.685 6.514
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.552 0.277 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.309 4.520
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.641 0.321 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.575 5.246
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.538 0.270 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.450 4.404
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (2211 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.358 0.679 199.9
48: (ns/day) (hour/ns)
48: Performance: 2.162 11.099
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.490 0.746 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.970 12.183
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.555 0.278 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.283 4.542
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.769 0.385 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.811 6.297
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.016 0.509 199.7
48: (ns/day) (hour/ns)
48: Performance: 2.888 8.312
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.459 0.730 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.011 11.934
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (3712 ms)
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (63991 ms total)
48:
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.672 0.336 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.365 5.498
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.636 0.319 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.606 5.210
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.673 0.337 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.355 5.510
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 3.347 1.674 199.9
48: (ns/day) (hour/ns)
48: Performance: 0.877 27.361
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.708 0.355 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.142 5.794
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.998 0.500 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.940 8.164
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (22966 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.662 0.331 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.433 5.413
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.661 0.331 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.441 5.405
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.608 0.305 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.816 4.983
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.715 0.358 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.103 5.850
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.806 0.404 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.637 6.599
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.967 0.484 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.034 7.911
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (21600 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.383 0.692 199.9
48: (ns/day) (hour/ns)
48: Performance: 2.122 11.308
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.652 0.326 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.500 5.333
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.786 0.394 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.732 6.431
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.081 0.541 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.715 8.839
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.804 0.403 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.646 6.583
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.726 0.364 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.039 5.942
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (22156 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.166 0.583 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.517 9.533
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.773 0.387 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.797 6.321
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.777 0.389 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.773 6.361
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.948 0.475 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.094 7.757
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.728 0.365 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.026 5.961
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.704 0.353 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.162 5.766
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (22066 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.548 0.276 198.8
48: (ns/day) (hour/ns)
48: Performance: 5.328 4.505
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.688 0.344 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.264 5.628
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.916 0.459 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.201 7.498
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.871 0.936 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.569 15.296
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.734 0.368 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.995 6.007
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.809 0.905 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.622 14.794
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (23720 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.780 0.391 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.761 6.381
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.694 0.348 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.224 5.682
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.878 0.440 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.340 7.186
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.039 0.520 199.7
48: (ns/day) (hour/ns)
48: Performance: 2.824 8.499
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.873 0.437 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.358 7.147
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.656 0.329 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.467 5.373
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (22013 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.773 0.387 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.795 6.323
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.875 0.438 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.352 7.159
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.610 0.306 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.802 4.998
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.602 0.302 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.862 4.936
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.681 0.342 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.298 5.583
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.594 0.298 199.3
48: (ns/day) (hour/ns)
48: Performance: 4.932 4.866
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (21658 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.029 0.515 199.6
48: (ns/day) (hour/ns)
48: Performance: 2.850 8.422
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.610 0.306 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.797 5.003
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.659 0.331 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.441 5.404
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.815 0.408 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.597 6.673
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.644 0.323 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.548 5.277
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.515 0.258 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.683 4.223
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (21763 ms)
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (177944 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 27 tests from 3 test cases ran. (244564 ms total)
48: [ PASSED ] 27 tests.
48/52 Test #48: MdrunMpiCoordinationTestsTwoRanks ... Passed 244.65 sec
test 49
Start 49: GmxapiExternalInterfaceTests
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
49: Test timeout computed to be: 600
49: [==========] Running 9 tests from 2 test cases.
49: [----------] Global test environment set-up.
49: [----------] 8 tests from GmxApiTest
49: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
49: Setting the LD random seed to -550927214
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.222 0.306 399.6
49: (ns/day) (hour/ns)
49: Performance: 1.656 14.497
49: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3514 ms)
49: [ RUN ] GmxApiTest.SystemConstruction
49: Setting the LD random seed to -30862741
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49: [ OK ] GmxApiTest.SystemConstruction (3208 ms)
49: [ RUN ] GmxApiTest.SaneVersionComparisons
49: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
49: [ RUN ] GmxApiTest.VersionNamed0_1_Features
49: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
49: [ RUN ] GmxApiTest.RunnerBasicMD
49: Setting the LD random seed to 251779571
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.304 0.326 399.6
49: (ns/day) (hour/ns)
49: Performance: 1.551 15.470
49: [ OK ] GmxApiTest.RunnerBasicMD (3535 ms)
49: [ RUN ] GmxApiTest.RunnerReinitialize
49: Setting the LD random seed to -1503348371
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49:
49: Received the remote INT/TERM signal, stopping within 50 steps
49:
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 2.057 0.515 399.7
49: (ns/day) (hour/ns)
49: Performance: 6.886 3.485
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.926 0.482 399.4
49: (ns/day) (hour/ns)
49: Performance: 7.349 3.266
49: [ OK ] GmxApiTest.RunnerReinitialize (4222 ms)
49: [ RUN ] GmxApiTest.RunnerContinuedMD
49: Setting the LD random seed to 854398011
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 10 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.420 0.356 399.5
49: (ns/day) (hour/ns)
49: Performance: 5.221 4.597
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.745 0.437 399.3
49: (ns/day) (hour/ns)
49: Performance: 8.109 2.960
49: [ OK ] GmxApiTest.RunnerContinuedMD (4011 ms)
49: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
49: Setting the LD random seed to 1316287747
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 1 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.824 0.456 399.7
49: (ns/day) (hour/ns)
49: Performance: 0.739 32.455
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.267 0.317 399.5
49: (ns/day) (hour/ns)
49: Performance: 1.064 22.563
49: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (3988 ms)
49: [----------] 8 tests from GmxApiTest (22480 ms total)
49:
49: [----------] 1 test from GmxApiBasicTest
49: [ RUN ] GmxApiBasicTest.Status
49: [ OK ] GmxApiBasicTest.Status (0 ms)
49: [----------] 1 test from GmxApiBasicTest (0 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 9 tests from 2 test cases ran. (22480 ms total)
49: [ PASSED ] 9 tests.
49/52 Test #49: GmxapiExternalInterfaceTests ........ Passed 22.56 sec
test 50
Start 50: GmxapiMpiTests
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiMpiTests.xml"
50: Test timeout computed to be: 600
50: [==========] Running 9 tests from 2 test cases.
50: [----------] Global test environment set-up.
50: [----------] 8 tests from GmxApiTest
50: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
50: Setting the LD random seed to -1490330186
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.344 0.336 399.7
50: (ns/day) (hour/ns)
50: Performance: 1.505 15.948
50: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3529 ms)
50: [ RUN ] GmxApiTest.SystemConstruction
50: Setting the LD random seed to -1063817887
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50: [ OK ] GmxApiTest.SystemConstruction (3245 ms)
50: [ RUN ] GmxApiTest.SaneVersionComparisons
50: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
50: [ RUN ] GmxApiTest.VersionNamed0_1_Features
50: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
50: [ RUN ] GmxApiTest.RunnerBasicMD
50: Setting the LD random seed to 618910653
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.089 0.273 399.6
50: (ns/day) (hour/ns)
50: Performance: 1.858 12.920
50: [ OK ] GmxApiTest.RunnerBasicMD (3519 ms)
50: [ RUN ] GmxApiTest.RunnerReinitialize
50: Setting the LD random seed to -453425563
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50:
50: Received the remote INT/TERM signal, stopping within 50 steps
50:
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.421 0.356 399.5
50: (ns/day) (hour/ns)
50: Performance: 9.962 2.409
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.427 0.358 399.2
50: (ns/day) (hour/ns)
50: Performance: 9.912 2.421
50: [ OK ] GmxApiTest.RunnerReinitialize (3967 ms)
50: [ RUN ] GmxApiTest.RunnerContinuedMD
50: Setting the LD random seed to -1862041990
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 10 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.497 0.375 399.6
50: (ns/day) (hour/ns)
50: Performance: 4.956 4.843
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.911 0.478 399.5
50: (ns/day) (hour/ns)
50: Performance: 7.407 3.240
50: [ OK ] GmxApiTest.RunnerContinuedMD (4077 ms)
50: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
50: Setting the LD random seed to 815436686
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 1 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.629 0.408 399.6
50: (ns/day) (hour/ns)
50: Performance: 0.828 28.984
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (single precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 3.382 0.846 399.8
50: (ns/day) (hour/ns)
50: Performance: 0.399 60.163
50: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4477 ms)
50: [----------] 8 tests from GmxApiTest (22816 ms total)
50:
50: [----------] 1 test from GmxApiBasicTest
50: [ RUN ] GmxApiBasicTest.Status
50: [ OK ] GmxApiBasicTest.Status (0 ms)
50: [----------] 1 test from GmxApiBasicTest (1 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 9 tests from 2 test cases ran. (22818 ms total)
50: [ PASSED ] 9 tests.
50/52 Test #50: GmxapiMpiTests ...................... Passed 22.90 sec
test 51
Start 51: GmxapiInternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 2 tests from 1 test case.
51: [----------] Global test environment set-up.
51: [----------] 2 tests from GmxApiTest
51: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
51: Setting the LD random seed to -1826186838
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.BuildApiWorkflowImpl (3135 ms)
51: [ RUN ] GmxApiTest.CreateApiWorkflow
51: Setting the LD random seed to 1779165158
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.CreateApiWorkflow (3113 ms)
51: [----------] 2 tests from GmxApiTest (6248 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 2 tests from 1 test case ran. (6249 ms total)
51: [ PASSED ] 2 tests.
51/52 Test #51: GmxapiInternalInterfaceTests ........ Passed 6.32 sec
test 52
Start 52: GmxapiInternalsMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalsMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 2 tests from 1 test case.
52: [----------] Global test environment set-up.
52: [----------] 2 tests from GmxApiTest
52: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
52: Setting the LD random seed to 332092481
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.BuildApiWorkflowImpl (3126 ms)
52: [ RUN ] GmxApiTest.CreateApiWorkflow
52: Setting the LD random seed to -449229165
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.CreateApiWorkflow (3116 ms)
52: [----------] 2 tests from GmxApiTest (6244 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 2 tests from 1 test case ran. (6246 ms total)
52: [ PASSED ] 2 tests.
52/52 Test #52: GmxapiInternalsMpiTests ............. Passed 6.32 sec
100% tests passed, 0 tests failed out of 52
Label Time Summary:
GTest = 962.48 sec*proc (52 tests)
IntegrationTest = 403.00 sec*proc (9 tests)
MpiTest = 663.16 sec*proc (8 tests)
SlowTest = 479.50 sec*proc (2 tests)
UnitTest = 79.97 sec*proc (41 tests)
Total Test time (real) = 963.04 sec
/usr/bin/make -j4 -C build/basic-dp tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 tests
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 96
/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.1-Raspbian-2020.1-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=/<<PKGBUILDDIR>>/src:/<<PKGBUILDDIR>>/python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.1-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target scanner
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
[ 0%] Built target release-version-info
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 2%] Built target thread_mpi
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
[ 3%] Built target lmfit_objlib
[ 3%] Built target tng_io_obj
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
[ 4%] Built target linearalgebra
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
[ 4%] Built target vmddlopen
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
Scanning dependencies of target gtest
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build
[ 4%] Built target mdrun_objlib
[ 5%] Built target modularsimulator
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 65%] Built target libgromacs
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 66%] Built target gmxapi
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 66%] Built target gtest
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
Scanning dependencies of target gmock
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 66%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o
/usr/bin/ranlib ../../lib/libtestutils.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
Scanning dependencies of target utility-mpi-test
Scanning dependencies of target testutils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target mdrun_test_infrastructure
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
[ 69%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdlib-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
Scanning dependencies of target utility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:331:51: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
331 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:333:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
333 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:377:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
377 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:379:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
379 | std::vector<real> constraintsR0 = { 2.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:384:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
384 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:388:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
388 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:390:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
390 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:431:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
431 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:438:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
438 | { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:440:101: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
440 | std::vector<RVec> xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:442:85: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
442 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:481:61: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
481 | std::vector<real> masses = { 12.0, 1.0, 1.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:483:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
483 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:488:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
488 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:493:59: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
493 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:495:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
495 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:534:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
534 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:541:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
541 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:545:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
545 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:547:106: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
547 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TriangleOfConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:594:63: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
594 | { 0.0, 0.0, oneTenthOverSqrtTwo } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:596:103: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
596 | std::vector<RVec> xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:598:88: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
598 | std::vector<RVec> v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target testutils-test
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
310 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::{anonymous}::iListInput; _Alloc = std::allocator<gmx::{anonymous}::iListInput>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' {aka '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:590:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
590 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:605:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
605 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:629:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
629 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:639:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
639 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:647:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
647 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:657:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
657 | std::vector<std::vector<gmx::RVec>> c_coordinatesForTests = {
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:657:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:657:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::integrateLeapFrogSimple(gmx::test::LeapFrogTestData*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::test::SettleTestData::SettleTestData(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<double> gmx::{anonymous}::computeDisplacements(const std::vector<int>&, const std::vector<double>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:79:80: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
79 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:118:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
118 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:146:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
146 | };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:650:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
650 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/9/bits/stl_vector.h:650:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:325:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
325 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
328 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:331:83: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
331 | c_sampleCoordinatesFull.begin() + 16);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function 'void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:201:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target hardware-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:77:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
77 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:84:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
84 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:94:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
94 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:104:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:115:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
115 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:125:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
125 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:133:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
133 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:134:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
134 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:142:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
142 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:143:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target gpu_utils-test
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target mdspan-test
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:188:5: note: in expansion of macro 'GMX_TEST_THROW_'
188 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::RVecTest_ConvertsImplicitlyFrom_rvec_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target table-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target options-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target simd-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target pdb2gmx2-test
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
Scanning dependencies of target analysisdata-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target correlations-test
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator' {aka '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In function 'void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function 'virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearch_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchBox_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function '{anonymous}::RandomBoxXYFullPBCData::RandomBoxXYFullPBCData()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:87:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
87 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:106:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:124:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target fileio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target selection-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-tpi-test
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-mpi-coordination-test
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target gmxapi-mpi-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target gmxapi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrun-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (5 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (3 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (3 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (26 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (3 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (5 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (103 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms)
1: [----------] 34 tests from ReferenceDataTest (152 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (8 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (189 ms total)
1: [ PASSED ] 59 tests.
1/52 Test #1: TestUtilsUnitTests .................. Passed 1.07 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (1 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (2 ms total)
2: [ PASSED ] 1 test.
2/52 Test #2: TestUtilsMpiUnitTests ............... Passed 0.07 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 346 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (2 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (2 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (2 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (2 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (2 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (1 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 3 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 3 tests from EnumerationHelpersTest (1 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (1 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (0 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (3 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
3: [----------] 6 tests from TreeValueTransformTest (4 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (0 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (2 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (3 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (7 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (1 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (2 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (3 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (2 ms)
3: [----------] 2 tests from PathTest (2 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (1 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (4 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (1 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (2 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms)
3: [----------] 10 tests from TextLineWrapperTest (6 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (1 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (1 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (3 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (2 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (3 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (3 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (3 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (2 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 346 tests from 56 test cases ran. (76 ms total)
3: [ PASSED ] 346 tests.
3/52 Test #3: UtilityUnitTests .................... Passed 0.20 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (13 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (15 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (16 ms total)
4: [ PASSED ] 2 tests.
4/52 Test #4: UtilityMpiUnitTests ................. Passed 0.08 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 149 tests from 11 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (2 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (2 ms)
5: [----------] 2 tests from PrEbinTest (4 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (0 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (0 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (1 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (0 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (1 ms)
5: [----------] 9 tests from UpdateGroups (2 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (16 ms)
5: [----------] 1 test from UpdateGroupsCog (16 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (20 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (46 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (12 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (3 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (51 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (16 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (18 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (16 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (15 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (16 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (236 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (42 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (11 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (147 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (7 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (8 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (7 ms)
5: [----------] 13 tests from WithParameters/SettleTest (54 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 149 tests from 11 test cases ran. (481 ms total)
5: [ PASSED ] 149 tests.
5/52 Test #5: MdlibUnitTest ....................... Passed 0.57 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (2 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (2 ms)
6: [----------] 2 tests from DensityFittingTest (4 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (1 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (5 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (1 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (1 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (0 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (1 ms)
6: [----------] 3 tests from ElectricFieldTest (2 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (13 ms total)
6: [ PASSED ] 20 tests.
6/52 Test #6: AppliedForcesUnitTest ............... Passed 0.09 sec
test 7
Start 7: ListedForcesTest
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ListedForcesTest.xml"
7: Test timeout computed to be: 30
7: [==========] Running 315 tests from 5 test cases.
7: [----------] Global test environment set-up.
7: [----------] 72 tests from Bond/ListedForcesTest
7: [ RUN ] Bond/ListedForcesTest.Ifunc/0
7: [ OK ] Bond/ListedForcesTest.Ifunc/0 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/1
7: [ OK ] Bond/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/2
7: [ OK ] Bond/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/3
7: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/4
7: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/5
7: [ OK ] Bond/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/6
7: [ OK ] Bond/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/7
7: [ OK ] Bond/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/8
7: [ OK ] Bond/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/9
7: [ OK ] Bond/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/10
7: [ OK ] Bond/ListedForcesTest.Ifunc/10 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/11
7: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/12
7: [ OK ] Bond/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/13
7: [ OK ] Bond/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/14
7: [ OK ] Bond/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/15
7: [ OK ] Bond/ListedForcesTest.Ifunc/15 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/16
7: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/17
7: [ OK ] Bond/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/18
7: [ OK ] Bond/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/19
7: [ OK ] Bond/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/20
7: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/21
7: [ OK ] Bond/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/22
7: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/23
7: [ OK ] Bond/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/24
7: [ OK ] Bond/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/25
7: [ OK ] Bond/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/26
7: [ OK ] Bond/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/27
7: [ OK ] Bond/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/28
7: [ OK ] Bond/ListedForcesTest.Ifunc/28 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/29
7: [ OK ] Bond/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/30
7: [ OK ] Bond/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/31
7: [ OK ] Bond/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/32
7: [ OK ] Bond/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/33
7: [ OK ] Bond/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/34
7: [ OK ] Bond/ListedForcesTest.Ifunc/34 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/35
7: [ OK ] Bond/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/36
7: [ OK ] Bond/ListedForcesTest.Ifunc/36 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/37
7: [ OK ] Bond/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/38
7: [ OK ] Bond/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/39
7: [ OK ] Bond/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/40
7: [ OK ] Bond/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/41
7: [ OK ] Bond/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/42
7: [ OK ] Bond/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/43
7: [ OK ] Bond/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/44
7: [ OK ] Bond/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/45
7: [ OK ] Bond/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/46
7: [ OK ] Bond/ListedForcesTest.Ifunc/46 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/47
7: [ OK ] Bond/ListedForcesTest.Ifunc/47 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/48
7: [ OK ] Bond/ListedForcesTest.Ifunc/48 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/49
7: [ OK ] Bond/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/50
7: [ OK ] Bond/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/51
7: [ OK ] Bond/ListedForcesTest.Ifunc/51 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/52
7: [ OK ] Bond/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/53
7: [ OK ] Bond/ListedForcesTest.Ifunc/53 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/54
7: [ OK ] Bond/ListedForcesTest.Ifunc/54 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/55
7: [ OK ] Bond/ListedForcesTest.Ifunc/55 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/56
7: [ OK ] Bond/ListedForcesTest.Ifunc/56 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/57
7: [ OK ] Bond/ListedForcesTest.Ifunc/57 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/58
7: [ OK ] Bond/ListedForcesTest.Ifunc/58 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/59
7: [ OK ] Bond/ListedForcesTest.Ifunc/59 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/60
7: [ OK ] Bond/ListedForcesTest.Ifunc/60 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/61
7: [ OK ] Bond/ListedForcesTest.Ifunc/61 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/62
7: [ OK ] Bond/ListedForcesTest.Ifunc/62 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/63
7: [ OK ] Bond/ListedForcesTest.Ifunc/63 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/64
7: [ OK ] Bond/ListedForcesTest.Ifunc/64 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/65
7: [ OK ] Bond/ListedForcesTest.Ifunc/65 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/66
7: [ OK ] Bond/ListedForcesTest.Ifunc/66 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/67
7: [ OK ] Bond/ListedForcesTest.Ifunc/67 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/68
7: [ OK ] Bond/ListedForcesTest.Ifunc/68 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/69
7: [ OK ] Bond/ListedForcesTest.Ifunc/69 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/70
7: [ OK ] Bond/ListedForcesTest.Ifunc/70 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/71
7: [ OK ] Bond/ListedForcesTest.Ifunc/71 (1 ms)
7: [----------] 72 tests from Bond/ListedForcesTest (83 ms total)
7:
7: [----------] 99 tests from Angle/ListedForcesTest
7: [ RUN ] Angle/ListedForcesTest.Ifunc/0
7: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/1
7: [ OK ] Angle/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/2
7: [ OK ] Angle/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/3
7: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/4
7: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/5
7: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/6
7: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/7
7: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/8
7: [ OK ] Angle/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/9
7: [ OK ] Angle/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/10
7: [ OK ] Angle/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/11
7: [ OK ] Angle/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/12
7: [ OK ] Angle/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/13
7: [ OK ] Angle/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/14
7: [ OK ] Angle/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/15
7: [ OK ] Angle/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/16
7: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/17
7: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/18
7: [ OK ] Angle/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/19
7: [ OK ] Angle/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/20
7: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/21
7: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/22
7: [ OK ] Angle/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/23
7: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/24
7: [ OK ] Angle/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/25
7: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/26
7: [ OK ] Angle/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/27
7: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/28
7: [ OK ] Angle/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/29
7: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/30
7: [ OK ] Angle/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/31
7: [ OK ] Angle/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/32
7: [ OK ] Angle/ListedForcesTest.Ifunc/32 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/33
7: [ OK ] Angle/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/34
7: [ OK ] Angle/ListedForcesTest.Ifunc/34 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/35
7: [ OK ] Angle/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/36
7: [ OK ] Angle/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/37
7: [ OK ] Angle/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/38
7: [ OK ] Angle/ListedForcesTest.Ifunc/38 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/39
7: [ OK ] Angle/ListedForcesTest.Ifunc/39 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/40
7: [ OK ] Angle/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/41
7: [ OK ] Angle/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/42
7: [ OK ] Angle/ListedForcesTest.Ifunc/42 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/43
7: [ OK ] Angle/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/44
7: [ OK ] Angle/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/45
7: [ OK ] Angle/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/46
7: [ OK ] Angle/ListedForcesTest.Ifunc/46 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/47
7: [ OK ] Angle/ListedForcesTest.Ifunc/47 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/48
7: [ OK ] Angle/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/49
7: [ OK ] Angle/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/50
7: [ OK ] Angle/ListedForcesTest.Ifunc/50 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/51
7: [ OK ] Angle/ListedForcesTest.Ifunc/51 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/52
7: [ OK ] Angle/ListedForcesTest.Ifunc/52 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/53
7: [ OK ] Angle/ListedForcesTest.Ifunc/53 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/54
7: [ OK ] Angle/ListedForcesTest.Ifunc/54 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/55
7: [ OK ] Angle/ListedForcesTest.Ifunc/55 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/56
7: [ OK ] Angle/ListedForcesTest.Ifunc/56 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/57
7: [ OK ] Angle/ListedForcesTest.Ifunc/57 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/58
7: [ OK ] Angle/ListedForcesTest.Ifunc/58 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/59
7: [ OK ] Angle/ListedForcesTest.Ifunc/59 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/60
7: [ OK ] Angle/ListedForcesTest.Ifunc/60 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/61
7: [ OK ] Angle/ListedForcesTest.Ifunc/61 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/62
7: [ OK ] Angle/ListedForcesTest.Ifunc/62 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/63
7: [ OK ] Angle/ListedForcesTest.Ifunc/63 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/64
7: [ OK ] Angle/ListedForcesTest.Ifunc/64 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/65
7: [ OK ] Angle/ListedForcesTest.Ifunc/65 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/66
7: [ OK ] Angle/ListedForcesTest.Ifunc/66 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/67
7: [ OK ] Angle/ListedForcesTest.Ifunc/67 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/68
7: [ OK ] Angle/ListedForcesTest.Ifunc/68 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/69
7: [ OK ] Angle/ListedForcesTest.Ifunc/69 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/70
7: [ OK ] Angle/ListedForcesTest.Ifunc/70 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/71
7: [ OK ] Angle/ListedForcesTest.Ifunc/71 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/72
7: [ OK ] Angle/ListedForcesTest.Ifunc/72 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/73
7: [ OK ] Angle/ListedForcesTest.Ifunc/73 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/74
7: [ OK ] Angle/ListedForcesTest.Ifunc/74 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/75
7: [ OK ] Angle/ListedForcesTest.Ifunc/75 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/76
7: [ OK ] Angle/ListedForcesTest.Ifunc/76 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/77
7: [ OK ] Angle/ListedForcesTest.Ifunc/77 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/78
7: [ OK ] Angle/ListedForcesTest.Ifunc/78 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/79
7: [ OK ] Angle/ListedForcesTest.Ifunc/79 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/80
7: [ OK ] Angle/ListedForcesTest.Ifunc/80 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/81
7: [ OK ] Angle/ListedForcesTest.Ifunc/81 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/82
7: [ OK ] Angle/ListedForcesTest.Ifunc/82 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/83
7: [ OK ] Angle/ListedForcesTest.Ifunc/83 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/84
7: [ OK ] Angle/ListedForcesTest.Ifunc/84 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/85
7: [ OK ] Angle/ListedForcesTest.Ifunc/85 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/86
7: [ OK ] Angle/ListedForcesTest.Ifunc/86 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/87
7: [ OK ] Angle/ListedForcesTest.Ifunc/87 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/88
7: [ OK ] Angle/ListedForcesTest.Ifunc/88 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/89
7: [ OK ] Angle/ListedForcesTest.Ifunc/89 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/90
7: [ OK ] Angle/ListedForcesTest.Ifunc/90 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/91
7: [ OK ] Angle/ListedForcesTest.Ifunc/91 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/92
7: [ OK ] Angle/ListedForcesTest.Ifunc/92 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/93
7: [ OK ] Angle/ListedForcesTest.Ifunc/93 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/94
7: [ OK ] Angle/ListedForcesTest.Ifunc/94 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/95
7: [ OK ] Angle/ListedForcesTest.Ifunc/95 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/96
7: [ OK ] Angle/ListedForcesTest.Ifunc/96 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/97
7: [ OK ] Angle/ListedForcesTest.Ifunc/97 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/98
7: [ OK ] Angle/ListedForcesTest.Ifunc/98 (0 ms)
7: [----------] 99 tests from Angle/ListedForcesTest (110 ms total)
7:
7: [----------] 54 tests from Dihedral/ListedForcesTest
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/18
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/18 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/19
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/20
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/21
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/21 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/22
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/22 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/23
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/24
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/25
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/25 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/26
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/27
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/28
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/29
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/30
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/31
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/31 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/32
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/33
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/34
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/35
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/36
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/36 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/37
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/38
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/38 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/39
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/40
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/40 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/41
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/42
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/43
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/44
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/45
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/46
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/47
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/47 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/48
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/48 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/49
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/50
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/50 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/51
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/51 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/52
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/52 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/53
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/53 (1 ms)
7: [----------] 54 tests from Dihedral/ListedForcesTest (59 ms total)
7:
7: [----------] 36 tests from Polarize/ListedForcesTest
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
7: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
7: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
7: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
7: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
7: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
7: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
7: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
7: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
7: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
7: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
7: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
7: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/12
7: [ OK ] Polarize/ListedForcesTest.Ifunc/12 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/13
7: [ OK ] Polarize/ListedForcesTest.Ifunc/13 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/14
7: [ OK ] Polarize/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/15
7: [ OK ] Polarize/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/16
7: [ OK ] Polarize/ListedForcesTest.Ifunc/16 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/17
7: [ OK ] Polarize/ListedForcesTest.Ifunc/17 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/18
7: [ OK ] Polarize/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/19
7: [ OK ] Polarize/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/20
7: [ OK ] Polarize/ListedForcesTest.Ifunc/20 (2 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/21
7: [ OK ] Polarize/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/22
7: [ OK ] Polarize/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/23
7: [ OK ] Polarize/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/24
7: [ OK ] Polarize/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/25
7: [ OK ] Polarize/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/26
7: [ OK ] Polarize/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/27
7: [ OK ] Polarize/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/28
7: [ OK ] Polarize/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/29
7: [ OK ] Polarize/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/30
7: [ OK ] Polarize/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/31
7: [ OK ] Polarize/ListedForcesTest.Ifunc/31 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/32
7: [ OK ] Polarize/ListedForcesTest.Ifunc/32 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/33
7: [ OK ] Polarize/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/34
7: [ OK ] Polarize/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/35
7: [ OK ] Polarize/ListedForcesTest.Ifunc/35 (1 ms)
7: [----------] 36 tests from Polarize/ListedForcesTest (32 ms total)
7:
7: [----------] 54 tests from Restraints/ListedForcesTest
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
7: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
7: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
7: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
7: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
7: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
7: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
7: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
7: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
7: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
7: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
7: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
7: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
7: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
7: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
7: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
7: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
7: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
7: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/18
7: [ OK ] Restraints/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/19
7: [ OK ] Restraints/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/20
7: [ OK ] Restraints/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/21
7: [ OK ] Restraints/ListedForcesTest.Ifunc/21 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/22
7: [ OK ] Restraints/ListedForcesTest.Ifunc/22 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/23
7: [ OK ] Restraints/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/24
7: [ OK ] Restraints/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/25
7: [ OK ] Restraints/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/26
7: [ OK ] Restraints/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/27
7: [ OK ] Restraints/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/28
7: [ OK ] Restraints/ListedForcesTest.Ifunc/28 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/29
7: [ OK ] Restraints/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/30
7: [ OK ] Restraints/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/31
7: [ OK ] Restraints/ListedForcesTest.Ifunc/31 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/32
7: [ OK ] Restraints/ListedForcesTest.Ifunc/32 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/33
7: [ OK ] Restraints/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/34
7: [ OK ] Restraints/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/35
7: [ OK ] Restraints/ListedForcesTest.Ifunc/35 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/36
7: [ OK ] Restraints/ListedForcesTest.Ifunc/36 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/37
7: [ OK ] Restraints/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/38
7: [ OK ] Restraints/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/39
7: [ OK ] Restraints/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/40
7: [ OK ] Restraints/ListedForcesTest.Ifunc/40 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/41
7: [ OK ] Restraints/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/42
7: [ OK ] Restraints/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/43
7: [ OK ] Restraints/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/44
7: [ OK ] Restraints/ListedForcesTest.Ifunc/44 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/45
7: [ OK ] Restraints/ListedForcesTest.Ifunc/45 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/46
7: [ OK ] Restraints/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/47
7: [ OK ] Restraints/ListedForcesTest.Ifunc/47 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/48
7: [ OK ] Restraints/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/49
7: [ OK ] Restraints/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/50
7: [ OK ] Restraints/ListedForcesTest.Ifunc/50 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/51
7: [ OK ] Restraints/ListedForcesTest.Ifunc/51 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/52
7: [ OK ] Restraints/ListedForcesTest.Ifunc/52 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/53
7: [ OK ] Restraints/ListedForcesTest.Ifunc/53 (1 ms)
7: [----------] 54 tests from Restraints/ListedForcesTest (66 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 315 tests from 5 test cases ran. (351 ms total)
7: [ PASSED ] 315 tests.
7/52 Test #7: ListedForcesTest .................... Passed 0.60 sec
test 8
Start 8: CommandLineUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 7 test cases.
8: [----------] Global test environment set-up.
8: [----------] 3 tests from CommandLineHelpModuleTest
8: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
8: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (4 ms)
8: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
8: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
8: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
8: [ OK ] CommandLineHelpModuleTest.ExportsHelp (5 ms)
8: [----------] 3 tests from CommandLineHelpModuleTest (12 ms total)
8:
8: [----------] 7 tests from CommandLineHelpWriterTest
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
8: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (2 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
8: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
8: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
8: [----------] 7 tests from CommandLineHelpWriterTest (10 ms total)
8:
8: [----------] 6 tests from CommandLineModuleManagerTest
8: [ RUN ] CommandLineModuleManagerTest.RunsModule
8: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
8: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
8: [----------] 6 tests from CommandLineModuleManagerTest (6 ms total)
8:
8: [----------] 13 tests from CommandLineParserTest
8: [ RUN ] CommandLineParserTest.HandlesSingleValues
8: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
8: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
8: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesString
8: [ OK ] CommandLineParserTest.HandlesString (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
8: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
8: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
8: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
8: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
8: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
8: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
8: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
8: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
8: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
8: [----------] 13 tests from CommandLineParserTest (6 ms total)
8:
8: [----------] 6 tests from CommandLineProgramContextTest
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (1 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
8: [----------] 6 tests from CommandLineProgramContextTest (3 ms total)
8:
8: [----------] 3 tests from OutputNamesTest
8: [ RUN ] OutputNamesTest.CanBeSuffixed
8: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
8: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
8: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
8: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
8: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
8: [----------] 3 tests from OutputNamesTest (1 ms total)
8:
8: [----------] 21 tests from ParseCommonArgsTest
8: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
8: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
8: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
8: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
8: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
8: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (1 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
8: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
8: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
8: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (1 ms)
8: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
8: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
8: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
8: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
8: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (4 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
8: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
8: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
8: [----------] 21 tests from ParseCommonArgsTest (19 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 7 test cases ran. (59 ms total)
8: [ PASSED ] 59 tests.
8/52 Test #8: CommandLineUnitTests ................ Passed 0.13 sec
test 9
Start 9: DomDecTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 9 tests from 2 test cases.
9: [----------] Global test environment set-up.
9: [----------] 7 tests from HashedMap
9: [ RUN ] HashedMap.InsertsFinds
9: [ OK ] HashedMap.InsertsFinds (0 ms)
9: [ RUN ] HashedMap.NegativeKeysWork
9: [ OK ] HashedMap.NegativeKeysWork (0 ms)
9: [ RUN ] HashedMap.InsertsErases
9: [ OK ] HashedMap.InsertsErases (0 ms)
9: [ RUN ] HashedMap.InsertsOrAssigns
9: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
9: [ RUN ] HashedMap.Clears
9: [ OK ] HashedMap.Clears (0 ms)
9: [ RUN ] HashedMap.LinkedEntries
9: [ OK ] HashedMap.LinkedEntries (0 ms)
9: [ RUN ] HashedMap.ResizesTable
9: [ OK ] HashedMap.ResizesTable (0 ms)
9: [----------] 7 tests from HashedMap (1 ms total)
9:
9: [----------] 2 tests from LocalAtomSetManager
9: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
9: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
9: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
9: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
9: [----------] 2 tests from LocalAtomSetManager (0 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 9 tests from 2 test cases ran. (2 ms total)
9: [ PASSED ] 9 tests.
9/52 Test #9: DomDecTests ......................... Passed 0.06 sec
test 10
Start 10: EwaldUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 257 tests from 10 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (14 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (23 ms total)
10:
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (92 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (13 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (13 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (17 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (17 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (32 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (17 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (17 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (17 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (18 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (18 ms)
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (496 ms total)
10:
10: [----------] 144 tests from SaneInput/PmeGatherTest
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
10: [----------] 144 tests from SaneInput/PmeGatherTest (293 ms total)
10:
10: [----------] 16 tests from SaneInput/PmeSolveTest
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (8 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (12 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (11 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (10 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (7 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (11 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (12 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (4 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (7 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (4 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (7 ms)
10: [----------] 16 tests from SaneInput/PmeSolveTest (122 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (4 ms)
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (42 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (12 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (11 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (7 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (10 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (10 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (69 ms total)
10:
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (10 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (10 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (7 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (11 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (11 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (6 ms)
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (108 ms total)
10:
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (11 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (31 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (11 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (10 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (16 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (13 ms)
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (137 ms total)
10:
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (11 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (13 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (18 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (15 ms)
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (148 ms total)
10:
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (17 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (19 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (26 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (28 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (36 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (40 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (17 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (18 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (33 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (27 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (33 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (38 ms)
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (356 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 257 tests from 10 test cases ran. (2486 ms total)
10: [ PASSED ] 257 tests.
10/52 Test #10: EwaldUnitTests ...................... Passed 2.72 sec
test 11
Start 11: FFTUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 14 tests from 4 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ManyFFTTest
11: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (42 ms)
11: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (38 ms)
11: [----------] 2 tests from ManyFFTTest (84 ms total)
11:
11: [----------] 1 test from FFTTest
11: [ RUN ] FFTTest.Real2DLength18_15Test
11: [ OK ] FFTTest.Real2DLength18_15Test (25 ms)
11: [----------] 1 test from FFTTest (26 ms total)
11:
11: [----------] 1 test from FFFTest3D
11: [ RUN ] FFFTest3D.Real5_6_9
11: [ OK ] FFFTest3D.Real5_6_9 (10 ms)
11: [----------] 1 test from FFFTest3D (12 ms total)
11:
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (2 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (2 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (6 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (9 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (31 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (43 ms)
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (109 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 14 tests from 4 test cases ran. (232 ms total)
11: [ PASSED ] 14 tests.
11/52 Test #11: FFTUnitTests ........................ Passed 0.30 sec
test 12
Start 12: GpuUtilsUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 62 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 2 tests from ClfftInitializer
12: [ RUN ] ClfftInitializer.SingleInitializationWorks
12: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
12: [ RUN ] ClfftInitializer.TwoInitializationsWork
12: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
12: [----------] 2 tests from ClfftInitializer (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
12: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
12: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (1 ms)
12: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/3 (1 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
12: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
12: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (1 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Swap
12: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Comparison
12: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
12: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
12: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Swap
12: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Comparison
12: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
12: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Swap
12: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Comparison
12: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
12: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Swap
12: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Comparison
12: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
12:
12: [----------] 1 test from HostAllocatorUntypedTest
12: [ RUN ] HostAllocatorUntypedTest.Comparison
12: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
12: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
12:
12: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.Move
12: [ OK ] AllocatorTest/0.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/0 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.Move
12: [ OK ] AllocatorTest/1.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/1 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (2 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.Move
12: [ OK ] AllocatorTest/2.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/2 (2 ms total)
12:
12: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.Move
12: [ OK ] AllocatorTest/3.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/3 (1 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 62 tests from 20 test cases ran. (9 ms total)
12: [ PASSED ] 62 tests.
12/52 Test #12: GpuUtilsUnitTests ................... Passed 0.09 sec
test 13
Start 13: HardwareUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 4 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 4 tests from HardwareTopologyTest
13: [ RUN ] HardwareTopologyTest.Execute
13: [ OK ] HardwareTopologyTest.Execute (34 ms)
13: [ RUN ] HardwareTopologyTest.HwlocExecute
13: [ OK ] HardwareTopologyTest.HwlocExecute (31 ms)
13: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
13: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (32 ms)
13: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
13: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (31 ms)
13: [----------] 4 tests from HardwareTopologyTest (131 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 4 tests from 1 test case ran. (132 ms total)
13: [ PASSED ] 4 tests.
13/52 Test #13: HardwareUnitTests ................... Passed 0.19 sec
test 14
Start 14: MathUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 204 tests from 29 test cases.
14: [----------] Global test environment set-up.
14: [----------] 1 test from EmptyArrayRefWithPaddingTest
14: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
14:
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
14: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
14: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
14: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (1 ms)
14: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/1 (1 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
14: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
14:
14: [----------] 8 tests from TranslateAndScaleTest
14: [ RUN ] TranslateAndScaleTest.identityTransformation
14: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms)
14: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
14: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (1 ms)
14: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
14: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
14: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
14: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingIdentity
14: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
14: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
14: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
14: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
14: [----------] 8 tests from TranslateAndScaleTest (2 ms total)
14:
14: [----------] 12 tests from DensitySimilarityTest
14: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (1 ms)
14: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
14: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
14: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (1 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (189 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (200 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (128 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
14: [----------] 12 tests from DensitySimilarityTest (520 ms total)
14:
14: [----------] 6 tests from StructureSimilarityTest
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
14: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
14: [----------] 6 tests from StructureSimilarityTest (0 ms total)
14:
14: [----------] 8 tests from ExponentialMovingAverage
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (1 ms)
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
14: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
14: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
14: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
14: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
14: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
14: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
14: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
14: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
14: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
14: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
14: [----------] 8 tests from ExponentialMovingAverage (1 ms total)
14:
14: [----------] 21 tests from FunctionTest
14: [ RUN ] FunctionTest.StaticLog2
14: [ OK ] FunctionTest.StaticLog2 (1 ms)
14: [ RUN ] FunctionTest.Log2I32Bit
14: [ OK ] FunctionTest.Log2I32Bit (0 ms)
14: [ RUN ] FunctionTest.Log2I64Bit
14: [ OK ] FunctionTest.Log2I64Bit (1 ms)
14: [ RUN ] FunctionTest.GreatestCommonDivisor
14: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
14: [ RUN ] FunctionTest.InvsqrtFloat
14: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
14: [ RUN ] FunctionTest.InvsqrtDouble
14: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
14: [ RUN ] FunctionTest.InvsqrtInteger
14: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
14: [ RUN ] FunctionTest.InvcbrtFloat
14: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
14: [ RUN ] FunctionTest.InvcbrtDouble
14: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
14: [ RUN ] FunctionTest.InvcbrtInteger
14: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
14: [ RUN ] FunctionTest.SixthrootFloat
14: [ OK ] FunctionTest.SixthrootFloat (1 ms)
14: [ RUN ] FunctionTest.SixthrootDouble
14: [ OK ] FunctionTest.SixthrootDouble (0 ms)
14: [ RUN ] FunctionTest.SixthrootInteger
14: [ OK ] FunctionTest.SixthrootInteger (1 ms)
14: [ RUN ] FunctionTest.InvsixthrootFloat
14: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
14: [ RUN ] FunctionTest.InvsixthrootDouble
14: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
14: [ RUN ] FunctionTest.InvsixthrootInteger
14: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
14: [ RUN ] FunctionTest.Powers
14: [ OK ] FunctionTest.Powers (0 ms)
14: [ RUN ] FunctionTest.ErfInvFloat
14: [ OK ] FunctionTest.ErfInvFloat (1 ms)
14: [ RUN ] FunctionTest.ErfInvDouble
14: [ OK ] FunctionTest.ErfInvDouble (0 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
14: [----------] 21 tests from FunctionTest (11 ms total)
14:
14: [----------] 4 tests from GaussianOn1DLattice
14: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
14: [ OK ] GaussianOn1DLattice.sumsCloseToOne (1 ms)
14: [ RUN ] GaussianOn1DLattice.isCorrect
14: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
14: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
14: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
14: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
14: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
14: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
14:
14: [----------] 9 tests from GaussTransformTest
14: [ RUN ] GaussTransformTest.isZeroUponConstruction
14: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
14: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
14: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
14: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
14: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
14: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
14: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
14: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
14: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
14: [ RUN ] GaussTransformTest.view
14: [ OK ] GaussTransformTest.view (1 ms)
14: [----------] 9 tests from GaussTransformTest (2 ms total)
14:
14: [----------] 3 tests from DensityFittingForce
14: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
14: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
14: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
14: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
14: [ RUN ] DensityFittingForce.pullsTowardsDerivative
14: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
14: [----------] 3 tests from DensityFittingForce (0 ms total)
14:
14: [----------] 2 tests from InvertMatrixTest
14: [ RUN ] InvertMatrixTest.IdentityIsImpotent
14: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertMatrixTest.ComputesInverse
14: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
14: [----------] 2 tests from InvertMatrixTest (0 ms total)
14:
14: [----------] 2 tests from InvertBoxMatrixTest
14: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
14: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
14: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
14: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
14:
14: [----------] 15 tests from MatrixTest
14: [ RUN ] MatrixTest.canSetFromArray
14: [ OK ] MatrixTest.canSetFromArray (0 ms)
14: [ RUN ] MatrixTest.canSetStaticallyFromList
14: [ OK ] MatrixTest.canSetStaticallyFromList (1 ms)
14: [ RUN ] MatrixTest.canConstructAndFill
14: [ OK ] MatrixTest.canConstructAndFill (0 ms)
14: [ RUN ] MatrixTest.canSetValues
14: [ OK ] MatrixTest.canSetValues (0 ms)
14: [ RUN ] MatrixTest.canCopyAssign
14: [ OK ] MatrixTest.canCopyAssign (0 ms)
14: [ RUN ] MatrixTest.canSwap
14: [ OK ] MatrixTest.canSwap (0 ms)
14: [ RUN ] MatrixTest.staticMultiDimArrayExtent
14: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MatrixTest.determinantWorks
14: [ OK ] MatrixTest.determinantWorks (0 ms)
14: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
14: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
14: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
14: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
14: [ RUN ] MatrixTest.traceWorks
14: [ OK ] MatrixTest.traceWorks (0 ms)
14: [ RUN ] MatrixTest.transposeWorks
14: [ OK ] MatrixTest.transposeWorks (0 ms)
14: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
14: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
14: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
14: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
14: [ RUN ] MatrixTest.canFillLegacyMatrix
14: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
14: [----------] 15 tests from MatrixTest (1 ms total)
14:
14: [----------] 25 tests from MultiDimArrayTest
14: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
14: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
14: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
14: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
14: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
14: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
14: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
14: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
14: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
14: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
14: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
14: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
14: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapStatic
14: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapDynamic
14: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToView
14: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToConstView
14: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
14: [ RUN ] MultiDimArrayTest.viewBegin
14: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.viewEnd
14: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstBegin
14: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstEnd
14: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
14: [----------] 25 tests from MultiDimArrayTest (1 ms total)
14:
14: [----------] 4 tests from MultiDimArrayToMdSpanTest
14: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
14: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
14: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanCopyAssign
14: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanMoveAssign
14: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanSwap
14: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
14: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanCopyAssign
14: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanMoveAssign
14: [ OK ] PaddedVectorTest/1.CanMoveAssign (1 ms)
14: [ RUN ] PaddedVectorTest/1.CanSwap
14: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/1 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
14: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanCopyAssign
14: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanMoveAssign
14: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanSwap
14: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
14: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanCopyAssign
14: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanMoveAssign
14: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanSwap
14: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
14: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanCopyAssign
14: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanMoveAssign
14: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanSwap
14: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/4 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanCopyAssign
14: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanMoveAssign
14: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanSwap
14: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanCopyAssign
14: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanMoveAssign
14: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanSwap
14: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanCopyAssign
14: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanMoveAssign
14: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanSwap
14: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/7 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanCopyAssign
14: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanMoveAssign
14: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanSwap
14: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanCopyAssign
14: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanMoveAssign
14: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanSwap
14: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
14:
14: [----------] 37 tests from RVecTest
14: [ RUN ] RVecTest.CanBeStoredInVector
14: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAsMutable_rvec
14: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Array
14: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
14: [ RUN ] RVecTest.CanAddRVecToRvec
14: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanAddAssignRVecToRvec
14: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractRVecFromRvec
14: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
14: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanDotProductRVecByRvec
14: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanCrossProductRVecByRvec
14: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVecInplace
14: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
14: [ RUN ] RVecTest.CanScaleRVec
14: [ OK ] RVecTest.CanScaleRVec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVec
14: [ OK ] RVecTest.CanDivideRVec (0 ms)
14: [ RUN ] RVecTest.CanDoUnitvFromRVec
14: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanSqLengthOfRVec
14: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanLengthOfRVec
14: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToRVec
14: [ OK ] RVecTest.CanCastToRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToDVec
14: [ OK ] RVecTest.CanCastToDVec (0 ms)
14: [ RUN ] RVecTest.CanLeftScalarMultiply
14: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanRightScalarMultiply
14: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanGetUnitvFromRVec
14: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanGetSqLengthOfRVec
14: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanGetLengthOfRVec
14: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoCrossProductOfRVec
14: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoDotProductOfRVec
14: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanScaleByVector
14: [ OK ] RVecTest.CanScaleByVector (0 ms)
14: [ RUN ] RVecTest.asIVec
14: [ OK ] RVecTest.asIVec (0 ms)
14: [ RUN ] RVecTest.elementWiseMin
14: [ OK ] RVecTest.elementWiseMin (0 ms)
14: [ RUN ] RVecTest.elementWiseMax
14: [ OK ] RVecTest.elementWiseMax (0 ms)
14: [ RUN ] RVecTest.WorksAs_dvec_Reference
14: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_ivec_Reference
14: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Reference
14: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
14: [ RUN ] RVecTest.CopyConstructorWorks
14: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
14: [ RUN ] RVecTest.CopyAssignmentWorks
14: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
14: [ RUN ] RVecTest.MoveConstructorWorks
14: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
14: [ RUN ] RVecTest.MoveAssignmentWorks
14: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
14: [----------] 37 tests from RVecTest (1 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 204 tests from 29 test cases ran. (548 ms total)
14: [ PASSED ] 204 tests.
14/52 Test #14: MathUnitTests ....................... Passed 0.64 sec
test 15
Start 15: MdrunUtilityUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 17 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 17 tests from ThreadAffinityTest
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
15: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (2 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
15: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (2 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (3 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
15: NOTE: Affinity setting failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
15: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
15: NOTE: Affinity setting for 1/2 threads failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
15: [----------] 17 tests from ThreadAffinityTest (21 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 17 tests from 1 test case ran. (22 ms total)
15: [ PASSED ] 17 tests.
15/52 Test #15: MdrunUtilityUnitTests ............... Passed 0.09 sec
test 16
Start 16: MdrunUtilityMpiUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 13 tests from 2 test cases.
16: [----------] Global test environment set-up.
16: [----------] 6 tests from ThreadAffinityMultiRankTest
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
16: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (63 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
16: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (54 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
16: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (86 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
16: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (23 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (54 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
16: [----------] 6 tests from ThreadAffinityMultiRankTest (288 ms total)
16:
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (10 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (140 ms)
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (174 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 13 tests from 2 test cases ran. (463 ms total)
16: [ PASSED ] 13 tests.
16/52 Test #16: MdrunUtilityMpiUnitTests ............ Passed 0.53 sec
test 17
Start 17: MDSpanTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 32 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from BasicAccessorPolicy
17: [ RUN ] BasicAccessorPolicy.Decay
17: [ OK ] BasicAccessorPolicy.Decay (0 ms)
17: [ RUN ] BasicAccessorPolicy.Access
17: [ OK ] BasicAccessorPolicy.Access (0 ms)
17: [ RUN ] BasicAccessorPolicy.Offset
17: [ OK ] BasicAccessorPolicy.Offset (0 ms)
17: [ RUN ] BasicAccessorPolicy.CopyAccessor
17: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
17: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
17:
17: [----------] 4 tests from ExtentsTest
17: [ RUN ] ExtentsTest.Construction
17: [ OK ] ExtentsTest.Construction (0 ms)
17: [ RUN ] ExtentsTest.PurelyStatic
17: [ OK ] ExtentsTest.PurelyStatic (0 ms)
17: [ RUN ] ExtentsTest.RankNought
17: [ OK ] ExtentsTest.RankNought (0 ms)
17: [ RUN ] ExtentsTest.Assignment
17: [ OK ] ExtentsTest.Assignment (0 ms)
17: [----------] 4 tests from ExtentsTest (0 ms total)
17:
17: [----------] 8 tests from MdSpanExtension
17: [ RUN ] MdSpanExtension.SlicingAllStatic
17: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingDynamic
17: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingAllStatic3D
17: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
17: [ RUN ] MdSpanExtension.SlicingEqualsView3D
17: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
17: [ RUN ] MdSpanExtension.additionWorks
17: [ OK ] MdSpanExtension.additionWorks (0 ms)
17: [ RUN ] MdSpanExtension.subtractionWorks
17: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
17: [ RUN ] MdSpanExtension.multiplicationWorks
17: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
17: [ RUN ] MdSpanExtension.divisionWorks
17: [ OK ] MdSpanExtension.divisionWorks (0 ms)
17: [----------] 8 tests from MdSpanExtension (0 ms total)
17:
17: [----------] 3 tests from LayoutTests
17: [ RUN ] LayoutTests.LayoutRightConstruction
17: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
17: [ RUN ] LayoutTests.LayoutRightProperties
17: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
17: [ RUN ] LayoutTests.LayoutRightOperator
17: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
17: [----------] 3 tests from LayoutTests (0 ms total)
17:
17: [----------] 1 test from MdSpanTest
17: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
17: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
17: [----------] 1 test from MdSpanTest (0 ms total)
17:
17: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
17: [ RUN ] MdSpanTest/0.Rank
17: [ OK ] MdSpanTest/0.Rank (0 ms)
17: [ RUN ] MdSpanTest/0.DynamicRank
17: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/0.Extents
17: [ OK ] MdSpanTest/0.Extents (0 ms)
17: [ RUN ] MdSpanTest/0.Strides
17: [ OK ] MdSpanTest/0.Strides (0 ms)
17: [ RUN ] MdSpanTest/0.Properties
17: [ OK ] MdSpanTest/0.Properties (0 ms)
17: [ RUN ] MdSpanTest/0.Operator
17: [ OK ] MdSpanTest/0.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/0 (0 ms total)
17:
17: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
17: [ RUN ] MdSpanTest/1.Rank
17: [ OK ] MdSpanTest/1.Rank (0 ms)
17: [ RUN ] MdSpanTest/1.DynamicRank
17: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/1.Extents
17: [ OK ] MdSpanTest/1.Extents (0 ms)
17: [ RUN ] MdSpanTest/1.Strides
17: [ OK ] MdSpanTest/1.Strides (0 ms)
17: [ RUN ] MdSpanTest/1.Properties
17: [ OK ] MdSpanTest/1.Properties (0 ms)
17: [ RUN ] MdSpanTest/1.Operator
17: [ OK ] MdSpanTest/1.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/1 (1 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 32 tests from 7 test cases ran. (3 ms total)
17: [ PASSED ] 32 tests.
17/52 Test #17: MDSpanTests ......................... Passed 0.08 sec
test 18
Start 18: OnlineHelpUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 22 tests from 4 test cases.
18: [----------] Global test environment set-up.
18: [----------] 6 tests from TextTableFormatterTest
18: [ RUN ] TextTableFormatterTest.HandlesBasicCase
18: [ OK ] TextTableFormatterTest.HandlesBasicCase (2 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesIndentation
18: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms)
18: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
18: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
18: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
18: [----------] 6 tests from TextTableFormatterTest (5 ms total)
18:
18: [----------] 3 tests from HelpManagerTest
18: [ RUN ] HelpManagerTest.HandlesRootTopic
18: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
18: [ RUN ] HelpManagerTest.HandlesSubTopics
18: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms)
18: [ RUN ] HelpManagerTest.HandlesInvalidTopics
18: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
18: [----------] 3 tests from HelpManagerTest (3 ms total)
18:
18: [----------] 2 tests from HelpTopicFormattingTest
18: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
18: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
18: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
18: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
18: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
18:
18: [----------] 11 tests from HelpWriterContextTest
18: [ RUN ] HelpWriterContextTest.FormatsParagraphs
18: [ OK ] HelpWriterContextTest.FormatsParagraphs (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
18: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
18: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
18: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralText
18: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsBulletList
18: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
18: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
18: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsGridTable
18: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsTitles
18: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
18: [----------] 11 tests from HelpWriterContextTest (7 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 22 tests from 4 test cases ran. (16 ms total)
18: [ PASSED ] 22 tests.
18/52 Test #18: OnlineHelpUnitTests ................. Passed 0.09 sec
test 19
Start 19: OptionsUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 110 tests from 18 test cases.
19: [----------] Global test environment set-up.
19: [----------] 5 tests from AbstractOptionStorageTest
19: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
19: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
19: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
19: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
19: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
19: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
19:
19: [----------] 8 tests from FileNameOptionTest
19: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
19: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
19: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
19: [----------] 8 tests from FileNameOptionTest (1 ms total)
19:
19: [----------] 15 tests from FileNameOptionManagerTest
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (1 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
19: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
19: [----------] 15 tests from FileNameOptionManagerTest (3 ms total)
19:
19: [----------] 1 test from OptionsTest
19: [ RUN ] OptionsTest.FailsOnNonsafeStorage
19: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
19: [----------] 1 test from OptionsTest (0 ms total)
19:
19: [----------] 9 tests from OptionsAssignerTest
19: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
19: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (1 ms)
19: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
19: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMissingValue
19: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesExtraValue
19: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesGroups
19: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesSections
19: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
19: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
19: [----------] 9 tests from OptionsAssignerTest (2 ms total)
19:
19: [----------] 4 tests from OptionsAssignerBooleanTest
19: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
19: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
19: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
19: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
19: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
19: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total)
19:
19: [----------] 13 tests from OptionsAssignerIntegerTest
19: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
19: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
19: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
19: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (1 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
19: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
19: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
19: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
19:
19: [----------] 5 tests from OptionsAssignerDoubleTest
19: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
19: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
19: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (1 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
19: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
19:
19: [----------] 9 tests from OptionsAssignerStringTest
19: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
19: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (1 ms)
19: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
19: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
19:
19: [----------] 6 tests from OptionsAssignerEnumTest
19: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
19: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
19: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
19: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
19:
19: [----------] 8 tests from RepeatingOptionSectionTest
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
19: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
19: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
19: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
19: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
19:
19: [----------] 1 test from TimeUnitManagerTest
19: [ RUN ] TimeUnitManagerTest.BasicOperations
19: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
19: [----------] 1 test from TimeUnitManagerTest (0 ms total)
19:
19: [----------] 4 tests from TimeUnitBehaviorTest
19: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
19: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (1 ms)
19: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
19: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
19: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
19: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
19: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
19:
19: [----------] 2 tests from TreeValueSupportAssignTest
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
19: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
19:
19: [----------] 1 test from TreeValueSupportAssignErrorTest
19: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
19: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (1 ms)
19: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total)
19:
19: [----------] 5 tests from TreeValueSupportCheckTest
19: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
19: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
19: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
19: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
19: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
19:
19: [----------] 6 tests from TreeValueSupportAdjustTest
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
19: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
19: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
19: [----------] 6 tests from TreeValueSupportAdjustTest (4 ms total)
19:
19: [----------] 8 tests from TreeValueSupportTest
19: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
19: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
19: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsInt64Option
19: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsStringOption
19: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsFloatOption
19: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
19: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
19: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumOption
19: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
19: [----------] 8 tests from TreeValueSupportTest (5 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 110 tests from 18 test cases ran. (26 ms total)
19: [ PASSED ] 110 tests.
19/52 Test #19: OptionsUnitTests .................... Passed 0.11 sec
test 20
Start 20: PbcutilUnitTest
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 2 test cases.
20: [----------] Global test environment set-up.
20: [----------] 1 test from PbcTest
20: [ RUN ] PbcTest.CalcShiftsWorks
20: [ OK ] PbcTest.CalcShiftsWorks (8 ms)
20: [----------] 1 test from PbcTest (8 ms total)
20:
20: [----------] 2 tests from PbcEnumsTest
20: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (1 ms)
20: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
20: [----------] 2 tests from PbcEnumsTest (1 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 2 test cases ran. (10 ms total)
20: [ PASSED ] 3 tests.
20/52 Test #20: PbcutilUnitTest ..................... Passed 0.08 sec
test 21
Start 21: RandomUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 44 tests from 10 test cases.
21: [----------] Global test environment set-up.
21: [----------] 4 tests from ExponentialDistributionTest
21: [ RUN ] ExponentialDistributionTest.Output
21: [ OK ] ExponentialDistributionTest.Output (11 ms)
21: [ RUN ] ExponentialDistributionTest.Logical
21: [ OK ] ExponentialDistributionTest.Logical (0 ms)
21: [ RUN ] ExponentialDistributionTest.Reset
21: [ OK ] ExponentialDistributionTest.Reset (0 ms)
21: [ RUN ] ExponentialDistributionTest.AltParam
21: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from ExponentialDistributionTest (11 ms total)
21:
21: [----------] 4 tests from GammaDistributionTest
21: [ RUN ] GammaDistributionTest.Output
21: [ OK ] GammaDistributionTest.Output (1 ms)
21: [ RUN ] GammaDistributionTest.Logical
21: [ OK ] GammaDistributionTest.Logical (0 ms)
21: [ RUN ] GammaDistributionTest.Reset
21: [ OK ] GammaDistributionTest.Reset (0 ms)
21: [ RUN ] GammaDistributionTest.AltParam
21: [ OK ] GammaDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from GammaDistributionTest (1 ms total)
21:
21: [----------] 4 tests from NormalDistributionTest
21: [ RUN ] NormalDistributionTest.Output
21: [ OK ] NormalDistributionTest.Output (0 ms)
21: [ RUN ] NormalDistributionTest.Logical
21: [ OK ] NormalDistributionTest.Logical (0 ms)
21: [ RUN ] NormalDistributionTest.Reset
21: [ OK ] NormalDistributionTest.Reset (0 ms)
21: [ RUN ] NormalDistributionTest.AltParam
21: [ OK ] NormalDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from NormalDistributionTest (1 ms total)
21:
21: [----------] 1 test from SeedTest
21: [ RUN ] SeedTest.makeRandomSeed
21: [ OK ] SeedTest.makeRandomSeed (0 ms)
21: [----------] 1 test from SeedTest (0 ms total)
21:
21: [----------] 6 tests from TabulatedNormalDistributionTest
21: [ RUN ] TabulatedNormalDistributionTest.Output14
21: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Output16
21: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
21: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Logical
21: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Reset
21: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.AltParam
21: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
21: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total)
21:
21: [----------] 1 test from TabulatedNormalDistributionTableTest
21: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
21: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (9 ms)
21: [----------] 1 test from TabulatedNormalDistributionTableTest (9 ms total)
21:
21: [----------] 6 tests from ThreeFry2x64Test
21: [ RUN ] ThreeFry2x64Test.Logical
21: [ OK ] ThreeFry2x64Test.Logical (0 ms)
21: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
21: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
21: [ RUN ] ThreeFry2x64Test.Reseed
21: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
21: [ RUN ] ThreeFry2x64Test.Discard
21: [ OK ] ThreeFry2x64Test.Discard (0 ms)
21: [ RUN ] ThreeFry2x64Test.InvalidCounter
21: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
21: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
21: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
21: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
21:
21: [----------] 4 tests from UniformIntDistributionTest
21: [ RUN ] UniformIntDistributionTest.Output
21: [ OK ] UniformIntDistributionTest.Output (0 ms)
21: [ RUN ] UniformIntDistributionTest.Logical
21: [ OK ] UniformIntDistributionTest.Logical (0 ms)
21: [ RUN ] UniformIntDistributionTest.Reset
21: [ OK ] UniformIntDistributionTest.Reset (0 ms)
21: [ RUN ] UniformIntDistributionTest.AltParam
21: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
21:
21: [----------] 5 tests from UniformRealDistributionTest
21: [ RUN ] UniformRealDistributionTest.GenerateCanonical
21: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
21: [ RUN ] UniformRealDistributionTest.Output
21: [ OK ] UniformRealDistributionTest.Output (0 ms)
21: [ RUN ] UniformRealDistributionTest.Logical
21: [ OK ] UniformRealDistributionTest.Logical (0 ms)
21: [ RUN ] UniformRealDistributionTest.Reset
21: [ OK ] UniformRealDistributionTest.Reset (0 ms)
21: [ RUN ] UniformRealDistributionTest.AltParam
21: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
21: [----------] 5 tests from UniformRealDistributionTest (2 ms total)
21:
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 44 tests from 10 test cases ran. (33 ms total)
21: [ PASSED ] 44 tests.
21/52 Test #21: RandomUnitTests ..................... Passed 0.13 sec
test 22
Start 22: RestraintTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 1 test from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 1 test from RestraintManager
22: [ RUN ] RestraintManager.restraintList
22: [ OK ] RestraintManager.restraintList (0 ms)
22: [----------] 1 test from RestraintManager (0 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 1 test from 1 test case ran. (0 ms total)
22: [ PASSED ] 1 test.
22/52 Test #22: RestraintTests ...................... Passed 0.06 sec
test 23
Start 23: TableUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 16 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
23: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectInput (7 ms)
23: [ RUN ] SplineTableTest/0.Sinc
23: [ OK ] SplineTableTest/0.Sinc (5 ms)
23: [ RUN ] SplineTableTest/0.LJ12
23: [ OK ] SplineTableTest/0.LJ12 (89 ms)
23: [ RUN ] SplineTableTest/0.PmeCorrection
23: [ OK ] SplineTableTest/0.PmeCorrection (7 ms)
23: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
23: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms)
23: [ RUN ] SplineTableTest/0.TwoFunctions
23: [ OK ] SplineTableTest/0.TwoFunctions (180 ms)
23: [ RUN ] SplineTableTest/0.ThreeFunctions
23: [ OK ] SplineTableTest/0.ThreeFunctions (219 ms)
23: [----------] 8 tests from SplineTableTest/0 (516 ms total)
23:
23: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
23: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectInput (6 ms)
23: [ RUN ] SplineTableTest/1.Sinc
23: [ OK ] SplineTableTest/1.Sinc (10 ms)
23: [ RUN ] SplineTableTest/1.LJ12
23: [ OK ] SplineTableTest/1.LJ12 (227 ms)
23: [ RUN ] SplineTableTest/1.PmeCorrection
23: [ OK ] SplineTableTest/1.PmeCorrection (8 ms)
23: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
23: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (5 ms)
23: [ RUN ] SplineTableTest/1.TwoFunctions
23: [ OK ] SplineTableTest/1.TwoFunctions (456 ms)
23: [ RUN ] SplineTableTest/1.ThreeFunctions
23: [ OK ] SplineTableTest/1.ThreeFunctions (542 ms)
23: [----------] 8 tests from SplineTableTest/1 (1258 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 16 tests from 2 test cases ran. (1774 ms total)
23: [ PASSED ] 16 tests.
23/52 Test #23: TableUnitTests ...................... Passed 1.84 sec
test 24
Start 24: TaskAssignmentUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 3 tests from 2 test cases.
24: [----------] Global test environment set-up.
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
24: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
24: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (2 ms)
24: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
24: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
24: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
24: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 3 tests from 2 test cases ran. (4 ms total)
24: [ PASSED ] 3 tests.
24/52 Test #24: TaskAssignmentUnitTests ............. Passed 0.07 sec
test 25
Start 25: TopologyTest
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 11 tests from 3 test cases.
25: [----------] Global test environment set-up.
25: [----------] 3 tests from ExclusionBlockTest
25: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
25: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
25: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
25: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
25: [ RUN ] ExclusionBlockTest.MergeExclusions
25: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
25: [----------] 3 tests from ExclusionBlockTest (0 ms total)
25:
25: [----------] 2 tests from MtopTest
25: [ RUN ] MtopTest.RangeBasedLoop
25: [ OK ] MtopTest.RangeBasedLoop (0 ms)
25: [ RUN ] MtopTest.Operators
25: [ OK ] MtopTest.Operators (0 ms)
25: [----------] 2 tests from MtopTest (0 ms total)
25:
25: [----------] 6 tests from SymtabTest
25: [ RUN ] SymtabTest.EmptyOnOpen
25: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
25: [ RUN ] SymtabTest.AddSingleEntry
25: [ OK ] SymtabTest.AddSingleEntry (0 ms)
25: [ RUN ] SymtabTest.AddTwoDistinctEntries
25: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
25: [ RUN ] SymtabTest.TryToAddDuplicates
25: [ OK ] SymtabTest.TryToAddDuplicates (1 ms)
25: [ RUN ] SymtabTest.AddLargeNumberOfEntries
25: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms)
25: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
25: [ OK ] SymtabTest.NoDuplicatesInLargeTable (1 ms)
25: [----------] 6 tests from SymtabTest (2 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 11 tests from 3 test cases ran. (3 ms total)
25: [ PASSED ] 11 tests.
25/52 Test #25: TopologyTest ........................ Passed 0.07 sec
test 26
Start 26: PullTest
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 5 tests from 1 test case.
26: [----------] Global test environment set-up.
26: [----------] 5 tests from PullTest
26: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
26: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
26: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
26: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
26: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
26: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
26: [----------] 5 tests from PullTest (1 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 5 tests from 1 test case ran. (1 ms total)
26: [ PASSED ] 5 tests.
26/52 Test #26: PullTest ............................ Passed 0.06 sec
test 27
Start 27: AwhTest
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
27: Test timeout computed to be: 30
27: [==========] Running 12 tests from 4 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from BiasTest
27: [ RUN ] BiasTest.DetectsCovering
27: [ OK ] BiasTest.DetectsCovering (4 ms)
27: [----------] 1 test from BiasTest (4 ms total)
27:
27: [----------] 1 test from gridTest
27: [ RUN ] gridTest.neighborhood
27: [ OK ] gridTest.neighborhood (9 ms)
27: [----------] 1 test from gridTest (9 ms total)
27:
27: [----------] 8 tests from WithParameters/BiasTest
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (2 ms)
27: [----------] 8 tests from WithParameters/BiasTest (20 ms total)
27:
27: [----------] 2 tests from WithParameters/BiasStateTest
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
27: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 12 tests from 4 test cases ran. (36 ms total)
27: [ PASSED ] 12 tests.
27/52 Test #27: AwhTest ............................. Passed 0.10 sec
test 28
Start 28: SimdUnitTests
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 86 tests from 3 test cases.
28: [----------] Global test environment set-up.
28: [----------] 41 tests from SimdScalarTest
28: [ RUN ] SimdScalarTest.load
28: [ OK ] SimdScalarTest.load (0 ms)
28: [ RUN ] SimdScalarTest.loadU
28: [ OK ] SimdScalarTest.loadU (0 ms)
28: [ RUN ] SimdScalarTest.store
28: [ OK ] SimdScalarTest.store (0 ms)
28: [ RUN ] SimdScalarTest.storeU
28: [ OK ] SimdScalarTest.storeU (0 ms)
28: [ RUN ] SimdScalarTest.setZero
28: [ OK ] SimdScalarTest.setZero (0 ms)
28: [ RUN ] SimdScalarTest.andNot
28: [ OK ] SimdScalarTest.andNot (0 ms)
28: [ RUN ] SimdScalarTest.fma
28: [ OK ] SimdScalarTest.fma (0 ms)
28: [ RUN ] SimdScalarTest.fms
28: [ OK ] SimdScalarTest.fms (0 ms)
28: [ RUN ] SimdScalarTest.fnma
28: [ OK ] SimdScalarTest.fnma (0 ms)
28: [ RUN ] SimdScalarTest.fnms
28: [ OK ] SimdScalarTest.fnms (0 ms)
28: [ RUN ] SimdScalarTest.maskAdd
28: [ OK ] SimdScalarTest.maskAdd (0 ms)
28: [ RUN ] SimdScalarTest.maskzMul
28: [ OK ] SimdScalarTest.maskzMul (0 ms)
28: [ RUN ] SimdScalarTest.maskzFma
28: [ OK ] SimdScalarTest.maskzFma (0 ms)
28: [ RUN ] SimdScalarTest.abs
28: [ OK ] SimdScalarTest.abs (0 ms)
28: [ RUN ] SimdScalarTest.max
28: [ OK ] SimdScalarTest.max (0 ms)
28: [ RUN ] SimdScalarTest.min
28: [ OK ] SimdScalarTest.min (0 ms)
28: [ RUN ] SimdScalarTest.round
28: [ OK ] SimdScalarTest.round (0 ms)
28: [ RUN ] SimdScalarTest.trunc
28: [ OK ] SimdScalarTest.trunc (0 ms)
28: [ RUN ] SimdScalarTest.reduce
28: [ OK ] SimdScalarTest.reduce (0 ms)
28: [ RUN ] SimdScalarTest.testBits
28: [ OK ] SimdScalarTest.testBits (0 ms)
28: [ RUN ] SimdScalarTest.anyTrue
28: [ OK ] SimdScalarTest.anyTrue (0 ms)
28: [ RUN ] SimdScalarTest.selectByMask
28: [ OK ] SimdScalarTest.selectByMask (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMask
28: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
28: [ RUN ] SimdScalarTest.blend
28: [ OK ] SimdScalarTest.blend (0 ms)
28: [ RUN ] SimdScalarTest.cvtR2I
28: [ OK ] SimdScalarTest.cvtR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvttR2I
28: [ OK ] SimdScalarTest.cvttR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvtI2R
28: [ OK ] SimdScalarTest.cvtI2R (0 ms)
28: [ RUN ] SimdScalarTest.cvtF2D
28: [ OK ] SimdScalarTest.cvtF2D (0 ms)
28: [ RUN ] SimdScalarTest.cvtD2D
28: [ OK ] SimdScalarTest.cvtD2D (0 ms)
28: [ RUN ] SimdScalarTest.loadI
28: [ OK ] SimdScalarTest.loadI (0 ms)
28: [ RUN ] SimdScalarTest.loadUI
28: [ OK ] SimdScalarTest.loadUI (0 ms)
28: [ RUN ] SimdScalarTest.storeI
28: [ OK ] SimdScalarTest.storeI (0 ms)
28: [ RUN ] SimdScalarTest.storeUI
28: [ OK ] SimdScalarTest.storeUI (0 ms)
28: [ RUN ] SimdScalarTest.andNotI
28: [ OK ] SimdScalarTest.andNotI (0 ms)
28: [ RUN ] SimdScalarTest.testBitsI
28: [ OK ] SimdScalarTest.testBitsI (0 ms)
28: [ RUN ] SimdScalarTest.selectByMaskI
28: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMaskI
28: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
28: [ RUN ] SimdScalarTest.blendI
28: [ OK ] SimdScalarTest.blendI (0 ms)
28: [ RUN ] SimdScalarTest.cvtB2IB
28: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
28: [ RUN ] SimdScalarTest.cvtIB2B
28: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
28: [ RUN ] SimdScalarTest.expandScalarsToTriplets
28: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
28: [----------] 41 tests from SimdScalarTest (2 ms total)
28:
28: [----------] 8 tests from SimdScalarUtilTest
28: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
28: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
28: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
28: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
28: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
28: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
28:
28: [----------] 37 tests from SimdScalarMathTest
28: [ RUN ] SimdScalarMathTest.copysign
28: [ OK ] SimdScalarMathTest.copysign (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPair
28: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
28: [ RUN ] SimdScalarMathTest.inv
28: [ OK ] SimdScalarMathTest.inv (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrt
28: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
28: [ RUN ] SimdScalarMathTest.log
28: [ OK ] SimdScalarMathTest.log (1 ms)
28: [ RUN ] SimdScalarMathTest.exp2
28: [ OK ] SimdScalarMathTest.exp2 (0 ms)
28: [ RUN ] SimdScalarMathTest.exp
28: [ OK ] SimdScalarMathTest.exp (0 ms)
28: [ RUN ] SimdScalarMathTest.erf
28: [ OK ] SimdScalarMathTest.erf (0 ms)
28: [ RUN ] SimdScalarMathTest.erfc
28: [ OK ] SimdScalarMathTest.erfc (0 ms)
28: [ RUN ] SimdScalarMathTest.sincos
28: [ OK ] SimdScalarMathTest.sincos (0 ms)
28: [ RUN ] SimdScalarMathTest.sin
28: [ OK ] SimdScalarMathTest.sin (0 ms)
28: [ RUN ] SimdScalarMathTest.cos
28: [ OK ] SimdScalarMathTest.cos (0 ms)
28: [ RUN ] SimdScalarMathTest.tan
28: [ OK ] SimdScalarMathTest.tan (0 ms)
28: [ RUN ] SimdScalarMathTest.asin
28: [ OK ] SimdScalarMathTest.asin (0 ms)
28: [ RUN ] SimdScalarMathTest.acos
28: [ OK ] SimdScalarMathTest.acos (0 ms)
28: [ RUN ] SimdScalarMathTest.atan
28: [ OK ] SimdScalarMathTest.atan (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2
28: [ OK ] SimdScalarMathTest.atan2 (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrection
28: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
28: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
28: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.invSingleAccuracy
28: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
28: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.logSingleAccuracy
28: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
28: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.expSingleAccuracy
28: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
28: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
28: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
28: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
28: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
28: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
28: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
28: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
28: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
28: [----------] 37 tests from SimdScalarMathTest (2 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 86 tests from 3 test cases ran. (5 ms total)
28: [ PASSED ] 86 tests.
28/52 Test #28: SimdUnitTests ....................... Passed 0.09 sec
test 29
Start 29: CompatibilityHelpersTests
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 170 tests from 12 test cases.
29: [----------] Global test environment set-up.
29: [----------] 45 tests from OptionalTest
29: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
29: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructEmpty
29: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
29: [ RUN ] OptionalTest.CanConstructFromNullopt
29: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
29: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
29: [ OK ] OptionalTest.CanCopyConstructFromLiteral (1 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
29: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValue
29: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
29: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValue
29: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
29: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
29: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
29: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromValue
29: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanMoveAssignFromValue
29: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanResetContent
29: [ OK ] OptionalTest.CanResetContent (0 ms)
29: [ RUN ] OptionalTest.ProvidesRelationalOperators
29: [ OK ] OptionalTest.ProvidesRelationalOperators (1 ms)
29: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
29: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms)
29: [ RUN ] OptionalTest.CanProduceHash
29: [ OK ] OptionalTest.CanProduceHash (0 ms)
29: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
29: alignment_of<char>: 1
29: alignment_of<short>: 2
29: alignment_of<int>: 4
29: alignment_of<long>: 4
29: alignment_of<float>: 4
29: alignment_of<double>: 8
29: alignment_of<long double>: 8
29: alignment_of<Struct>: 1
29: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (1 ms)
29: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
29: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
29: sizeof( optional<char> ): 2 (1)
29: sizeof( optional<short> ): 4 (2)
29: sizeof( optional<int> ): 8 (4)
29: sizeof( optional<long> ): 8 (4)
29: sizeof( optional<float> ): 8 (4)
29: sizeof( optional<double> ): 16 (8)
29: sizeof( optional<long double> ): 16 (8)
29: sizeof( optional<Struct> ): 2 (1)
29: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
29: [----------] 45 tests from OptionalTest (5 ms total)
29:
29: [----------] 7 tests from MakeOptionalTest
29: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
29: [ RUN ] MakeOptionalTest.CanCopyConstruct
29: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanMoveConstruct
29: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
29: [----------] 7 tests from MakeOptionalTest (0 ms total)
29:
29: [----------] 4 tests from OptionalMemberSwapTest
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
29: [----------] 4 tests from OptionalMemberSwapTest (1 ms total)
29:
29: [----------] 4 tests from OptionalImplicitValueTest
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
29: [----------] 4 tests from OptionalImplicitValueTest (0 ms total)
29:
29: [----------] 20 tests from OptionalIntValueTest
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
29: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
29: [----------] 20 tests from OptionalIntValueTest (2 ms total)
29:
29: [----------] 1 test from NotNullConstruction
29: [ RUN ] NotNullConstruction.Works
29: [ OK ] NotNullConstruction.Works (0 ms)
29: [----------] 1 test from NotNullConstruction (0 ms total)
29:
29: [----------] 1 test from NotNullCasting
29: [ RUN ] NotNullCasting.Works
29: [ OK ] NotNullCasting.Works (0 ms)
29: [----------] 1 test from NotNullCasting (0 ms total)
29:
29: [----------] 1 test from NotNullAssignment
29: [ RUN ] NotNullAssignment.Works
29: [ OK ] NotNullAssignment.Works (0 ms)
29: [----------] 1 test from NotNullAssignment (0 ms total)
29:
29: [----------] 1 test from MakeNotNull
29: [ RUN ] MakeNotNull.Works
29: [ OK ] MakeNotNull.Works (0 ms)
29: [----------] 1 test from MakeNotNull (0 ms total)
29:
29: [----------] 1 test from NotNull
29: [ RUN ] NotNull.WorksInContainers
29: [ OK ] NotNull.WorksInContainers (0 ms)
29: [----------] 1 test from NotNull (0 ms total)
29:
29: [----------] 80 tests from StringViewTest
29: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
29: [ OK ] StringViewTest.CanDefaultConstructEmptyView (1 ms)
29: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
29: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
29: [ RUN ] StringViewTest.CanConstructFromCString
29: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
29: [ RUN ] StringViewTest.AllowForwardIteration
29: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstForwardIteration
29: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowReverseIteration
29: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstReverseIteration
29: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
29: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
29: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
29: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
29: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
29: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaAt
29: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
29: [ RUN ] StringViewTest.CanAccessAllElementsViaData
29: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
29: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
29: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
29: [ RUN ] StringViewTest.CanRemovePrefix
29: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
29: [ RUN ] StringViewTest.CanRemoveSuffix
29: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
29: [ RUN ] StringViewTest.CanSwapWithOtherView
29: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
29: [ RUN ] StringViewTest.CanCopySubstringWithCopy
29: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
29: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
29: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (1 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
29: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
29: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
29: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCompareToViews
29: [ OK ] StringViewTest.CanCompareToViews (0 ms)
29: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
29: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
29: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
29: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
29: [ RUN ] StringViewTest.CanPrintViewToPutputStream
29: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
29: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
29: [----------] 80 tests from StringViewTest (6 ms total)
29:
29: [----------] 5 tests from StringViewExtensionTest
29: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
29: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
29: [----------] 5 tests from StringViewExtensionTest (1 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 170 tests from 12 test cases ran. (15 ms total)
29: [ PASSED ] 170 tests.
29/52 Test #29: CompatibilityHelpersTests ........... Passed 0.10 sec
test 30
Start 30: GmxAnaTest
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
30: Test timeout computed to be: 600
30: [==========] Running 27 tests from 5 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from Entropy
30: [ RUN ] Entropy.Schlitter_300_NoLinear
30: [ OK ] Entropy.Schlitter_300_NoLinear (171 ms)
30: [ RUN ] Entropy.Schlitter_300_Linear
30: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
30: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_Linear
30: [ OK ] Entropy.QuasiHarmonic_200_Linear (1 ms)
30: [----------] 5 tests from Entropy (174 ms total)
30:
30: [----------] 10 tests from MindistTest
30: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistWorksWithSingleAtoms (8 ms)
30: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (6 ms)
30: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms)
30: [ RUN ] MindistTest.mindistPicksUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistPicksUpContacts (6 ms)
30: [ RUN ] MindistTest.ngWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.ngWorks (5 ms)
30: [ RUN ] MindistTest.groupWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.groupWorks (7 ms)
30: [ RUN ] MindistTest.maxDistWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.maxDistWorks (5 ms)
30: [ RUN ] MindistTest.noPbcWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.noPbcWorks (6 ms)
30: [ RUN ] MindistTest.resPerTimeWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.resPerTimeWorks (6 ms)
30: [ RUN ] MindistTest.matrixWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 5: 'atoms123'
30: Special case: making distance matrix between all atoms in group atoms123
30: [ OK ] MindistTest.matrixWorks (6 ms)
30: [----------] 10 tests from MindistTest (62 ms total)
30:
30: [----------] 3 tests from MsdTest
30: [ RUN ] MsdTest.threeDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.threeDimensionalDiffusion (6 ms)
30: [ RUN ] MsdTest.twoDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.twoDimensionalDiffusion (5 ms)
30: [ RUN ] MsdTest.oneDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.oneDimensionalDiffusion (6 ms)
30: [----------] 3 tests from MsdTest (18 ms total)
30:
30: [----------] 3 tests from MsdMolTest
30: [ RUN ] MsdMolTest.diffMolMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -1844266395
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolMassWeighted (4100 ms)
30: [ RUN ] MsdMolTest.diffMolNonMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -2092624524
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolNonMassWeighted (4065 ms)
30: [ RUN ] MsdMolTest.diffMolSelected
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 1076408850
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( mol) has 9 elements
30: There is one group in the index
30: Split group of 9 atoms into 3 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolSelected (4022 ms)
30: [----------] 3 tests from MsdMolTest (12187 ms total)
30:
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: trr version: GMX_trn_file (single precision)
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (8 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (9 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (8 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from gro file '', 6 atoms.
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (8 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
30:
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (7 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (8 ms)
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (48 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 27 tests from 5 test cases ran. (12491 ms total)
30: [ PASSED ] 27 tests.
30/52 Test #30: GmxAnaTest .......................... Passed 12.57 sec
test 31
Start 31: GmxPreprocessTests
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
31: Test timeout computed to be: 30
31: [==========] Running 50 tests from 8 test cases.
31: [----------] Global test environment set-up.
31: [----------] 4 tests from GenconfTest
31: [ RUN ] GenconfTest.nbox_Works
31: [ OK ] GenconfTest.nbox_Works (26 ms)
31: [ RUN ] GenconfTest.nbox_norenumber_Works
31: [ OK ] GenconfTest.nbox_norenumber_Works (3 ms)
31: [ RUN ] GenconfTest.nbox_dist_Works
31: [ OK ] GenconfTest.nbox_dist_Works (4 ms)
31: [ RUN ] GenconfTest.nbox_rot_Works
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: [ OK ] GenconfTest.nbox_rot_Works (6 ms)
31: [----------] 4 tests from GenconfTest (39 ms total)
31:
31: [----------] 2 tests from GenionTest
31: [ RUN ] GenionTest.HighConcentrationIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to 1649965267
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
31: Group 0 ( System) has 653 elements
31: Group 1 ( Water) has 648 elements
31: Group 2 ( SOL) has 648 elements
31: Group 3 ( non-Water) has 5 elements
31: Group 4 ( Other) has 5 elements
31: Group 5 ( METH) has 5 elements
31: Select a group: Number of (3-atomic) solvent molecules: 216
31: Using random seed 1997.
31: Replacing solvent molecule 56 (atom 168) with NA
31: Replacing solvent molecule 120 (atom 360) with NA
31: Replacing solvent molecule 182 (atom 546) with NA
31: Replacing solvent molecule 71 (atom 213) with NA
31: Replacing solvent molecule 189 (atom 567) with CL
31: Replacing solvent molecule 54 (atom 162) with CL
31: Replacing solvent molecule 155 (atom 465) with CL
31: Replacing solvent molecule 99 (atom 297) with CL
31:
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: Will try to add 4 NA ions and 4 CL ions.
31: Select a continuous group of solvent molecules
31: Selected 1: 'Water'
31: [ OK ] GenionTest.HighConcentrationIonPlacement (4199 ms)
31: [ RUN ] GenionTest.NoIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to -231951357
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
31: No ions to add, will just copy input configuration.
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: [ OK ] GenionTest.NoIonPlacement (4100 ms)
31: [----------] 2 tests from GenionTest (8299 ms total)
31:
31: [----------] 9 tests from PreprocessingAtomTypesTest
31: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
31: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
31: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (1 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
31: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total)
31:
31: [----------] 10 tests from PreprocessingBondAtomTypeTest
31: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
31: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
31: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
31: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
31:
31: [----------] 5 tests from InsertMoleculesTest
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
31: Added 1 molecules (out of 1 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
31:
31: Output configuration contains 8 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (34 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3 success (now 6 atoms)!
31:
Try 4 success (now 8 atoms)!
31:
Try 5 success (now 10 atoms)!
31:
31: Added 5 molecules (out of 5 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
31:
31: Output configuration contains 10 atoms in 10 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (8 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
Try 2 success (now 10 atoms)!
31:
31: Added 2 molecules (out of 2 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
31:
31: Output configuration contains 10 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (9 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 650 atoms)!
31:
Try 2 success (now 652 atoms)!
31:
Try 3 success (now 654 atoms)!
31:
Try 4 success (now 656 atoms)!
31:
31: Added 4 molecules (out of 4 requested)
31: Replaced 8 residues (24 atoms)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
31:
31: Output configuration contains 632 atoms in 212 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (91 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
31:
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
31:
Try 13 success (now 6 atoms)!
31:
31: Added 3 molecules (out of 4 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
31:
31: Output configuration contains 6 atoms in 3 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (9 ms)
31: [----------] 5 tests from InsertMoleculesTest (151 ms total)
31:
31: [----------] 14 tests from GetIrTest
31: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
31: Ignoring obsolete mdp entry 'title'
31: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (37 ms)
31: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
31: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (30 ms)
31: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsKeyWithoutValue (24 ms)
31: [ RUN ] GetIrTest.RejectsValueWithoutKey
31: [ OK ] GetIrTest.RejectsValueWithoutKey (29 ms)
31: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
31: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (30 ms)
31: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (23 ms)
31: [ RUN ] GetIrTest.AcceptsEmptyLines
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsEmptyLines (19 ms)
31: [ RUN ] GetIrTest.AcceptsElectricField
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricField (25 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (32 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (30 ms)
31: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
31: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (13 ms)
31: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsImplicitSolventNo (29 ms)
31: [ RUN ] GetIrTest.RejectsImplicitSolventYes
31: [ OK ] GetIrTest.RejectsImplicitSolventYes (29 ms)
31: [ RUN ] GetIrTest.AcceptsMimic
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsMimic (20 ms)
31: [----------] 14 tests from GetIrTest (371 ms total)
31:
31: [----------] 5 tests from SolvateTest
31: [ RUN ] SolvateTest.cs_box_Works
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 1x1x1 boxes
31: Solvent box contains 270 atoms in 90 residues
31: Removed 129 solvent atoms due to solvent-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 47 residues
31: Generated solvent containing 141 atoms in 47 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
31:
31: Output configuration contains 141 atoms in 47 residues
31: Volume : 1.331 (nm^3)
31: Density : 1056.36 (g/l)
31: Number of solvent molecules: 47
31:
31: [ OK ] SolvateTest.cs_box_Works (62 ms)
31: [ RUN ] SolvateTest.cs_cp_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: [ OK ] SolvateTest.cs_cp_Works (274 ms)
31: [ RUN ] SolvateTest.cs_cp_p_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: Processing topology
31: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
31: [ OK ] SolvateTest.cs_cp_p_Works (298 ms)
31: [ RUN ] SolvateTest.shell_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 1902 solvent atoms more than 1.000000 nm from solute.
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 252 residues
31: Generated solvent containing 756 atoms in 252 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
31:
31: Output configuration contains 762 atoms in 254 residues
31: Volume : 27.2709 (nm^3)
31: Density : 279.3 (g/l)
31: Number of solvent molecules: 252
31:
31: [ OK ] SolvateTest.shell_Works (134 ms)
31: [ RUN ] SolvateTest.update_Topology_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 3x3x3 boxes
31: Solvent box contains 14952 atoms in 4984 residues
31: Removed 2787 solvent atoms due to solvent-solvent overlap
31: Removed 30 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 2 different molecule types:
31: HOH ( 3 atoms): 1876 residues
31: SOL ( 3 atoms): 2169 residues
31: Generated solvent containing 0 atoms in 0 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
31:
31: Output configuration contains 12141 atoms in 4047 residues
31: Volume : 125 (nm^3)
31: Density : 968.963 (g/l)
31: Number of solvent molecules: 4045
31:
31: Processing topology
31: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: [ OK ] SolvateTest.update_Topology_Works (1120 ms)
31: [----------] 5 tests from SolvateTest (1889 ms total)
31:
31: [----------] 1 test from TopDirTests
31: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
31: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
31: [----------] 1 test from TopDirTests (0 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 50 tests from 8 test cases ran. (10752 ms total)
31: [ PASSED ] 50 tests.
31/52 Test #31: GmxPreprocessTests .................. Passed 10.83 sec
test 32
Start 32: Pdb2gmx1Test
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 24 tests from 1 test case.
32: [----------] Global test environment set-up.
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (525 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (579 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (586 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (580 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (562 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (625 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (569 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (498 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (509 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (570 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (507 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (485 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (546 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (614 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (575 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (499 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (513 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (558 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (513 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (475 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (535 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (590 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (569 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (518 ms)
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (13106 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 24 tests from 1 test case ran. (13107 ms total)
32: [ PASSED ] 24 tests.
32/52 Test #32: Pdb2gmx1Test ........................ Passed 13.18 sec
test 33
Start 33: Pdb2gmx2Test
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 32 tests from 2 test cases.
33: [----------] Global test environment set-up.
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (313 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (351 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (309 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (286 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (315 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (383 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (335 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (311 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (308 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (363 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (333 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (295 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (329 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (374 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (361 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (316 ms)
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (5284 ms total)
33:
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (341 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (382 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (354 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (315 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (367 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (395 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (351 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (328 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (332 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (383 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (340 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (317 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (346 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (397 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (348 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (328 ms)
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (5626 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 32 tests from 2 test cases ran. (10910 ms total)
33: [ PASSED ] 32 tests.
33/52 Test #33: Pdb2gmx2Test ........................ Passed 10.98 sec
test 34
Start 34: Pdb2gmx3Test
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
34: Test timeout computed to be: 30
34: [==========] Running 28 tests from 4 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (490 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (492 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (442 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (407 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (464 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (533 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (492 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (435 ms)
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (3757 ms total)
34:
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (421 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (472 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (422 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (405 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (453 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (501 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (481 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (422 ms)
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (3579 ms total)
34:
34: [----------] 8 tests from ChainSep/Pdb2gmxTest
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (428 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 7 acceptors were found.
34: There are 7 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS8
34: NE223
34: MET12 SD55 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 125, now 125
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 317 pairs
34: Before cleaning: 322 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 5 cmap torsion pairs
34: There are 322 dihedrals, 19 impropers, 227 angles
34: 314 pairs, 125 bonds and 0 virtual sites
34: Total mass 846.083 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 7 58
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (58 atoms, 7 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 7 residues with 124 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 124 atoms 7 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (293 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (456 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 12 acceptors were found.
34: There are 13 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3
34: SG9
34: HIS8 NE251 1.055
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 115, now 115
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 288 pairs
34: Before cleaning: 293 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 6 cmap torsion pairs
34: There are 293 dihedrals, 23 impropers, 203 angles
34: 285 pairs, 115 bonds and 0 virtual sites
34: Total mass 888.952 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 8 61
34: 2 'B' 3 25
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (61 atoms, 8 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 8 residues with 114 atoms
34: Chain time...
34: Processing chain 2 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 114 atoms 8 residues
34: Including chain 2 in system: 61 atoms 3 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (297 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 260, now 260
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 650 pairs
34: Before cleaning: 660 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 8 cmap torsion pairs
34: There are 660 dihedrals, 45 impropers, 466 angles
34: 647 pairs, 260 bonds and 0 virtual sites
34: Total mass 1900.162 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34:
34: Merged chains into joint molecule definitions at 3 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 261 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (446 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 6 donors and 4 acceptors were found.
34: There are 3 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 67, now 67
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 164 pairs
34: Before cleaning: 169 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 169 dihedrals, 13 impropers, 118 angles
34: 161 pairs, 67 bonds and 0 virtual sites
34: Total mass 472.547 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 261 atoms and 16 residues
34: Total mass in system 1900.162 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
34: They will be treated as separate chains unless you reorder your file.
34: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 4 33
34: 3 'B' 3 25
34: 4 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (33 atoms, 4 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 66 atoms
34: Chain time...
34: Processing chain 3 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 4 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 66 atoms 4 residues
34: Including chain 3 in system: 61 atoms 3 residues
34: Including chain 4 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (289 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 256, now 256
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 652 pairs
34: Before cleaning: 662 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 12 cmap torsion pairs
34: There are 662 dihedrals, 47 impropers, 460 angles
34: 649 pairs, 256 bonds and 0 virtual sites
34: Total mass 1864.131 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34:
34: Merged chains into joint molecule definitions at 1 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (458 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 14 donors and 15 acceptors were found.
34: There are 20 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 173, now 173
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 441 pairs
34: Before cleaning: 446 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 9 cmap torsion pairs
34: There are 446 dihedrals, 29 impropers, 312 angles
34: 438 pairs, 173 bonds and 0 virtual sites
34: Total mass 1262.488 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 255 atoms and 16 residues
34: Total mass in system 1864.131 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 11 86
34: 2 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (86 atoms, 11 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 11 residues with 172 atoms
34: Chain time...
34: Processing chain 2 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 172 atoms 11 residues
34: Including chain 2 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (308 ms)
34: [----------] 8 tests from ChainSep/Pdb2gmxTest (2975 ms total)
34:
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (212 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (233 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (210 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (238 ms)
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest (893 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 28 tests from 4 test cases ran. (11205 ms total)
34: [ PASSED ] 28 tests.
34/52 Test #34: Pdb2gmx3Test ........................ Passed 11.28 sec
test 35
Start 35: CorrelationsTest
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
35: Test timeout computed to be: 30
35: [==========] Running 11 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 10 tests from AutocorrTest
35: [ RUN ] AutocorrTest.EacNormal
35: [ OK ] AutocorrTest.EacNormal (25 ms)
35: [ RUN ] AutocorrTest.EacNoNormalize
35: [ OK ] AutocorrTest.EacNoNormalize (13 ms)
35: [ RUN ] AutocorrTest.EacCos
35: [ OK ] AutocorrTest.EacCos (19 ms)
35: [ RUN ] AutocorrTest.EacVector
35: [ OK ] AutocorrTest.EacVector (25 ms)
35: [ RUN ] AutocorrTest.EacRcross
35: [ OK ] AutocorrTest.EacRcross (9 ms)
35: [ RUN ] AutocorrTest.EacP0
35: [ OK ] AutocorrTest.EacP0 (39 ms)
35: [ RUN ] AutocorrTest.EacP1
35: [ OK ] AutocorrTest.EacP1 (41 ms)
35: [ RUN ] AutocorrTest.EacP2
35: [ OK ] AutocorrTest.EacP2 (46 ms)
35: [ RUN ] AutocorrTest.EacP3
35: [ OK ] AutocorrTest.EacP3 (21 ms)
35: [ RUN ] AutocorrTest.EacP4
35: [ OK ] AutocorrTest.EacP4 (25 ms)
35: [----------] 10 tests from AutocorrTest (268 ms total)
35:
35: [----------] 1 test from ManyAutocorrelationTest
35: [ RUN ] ManyAutocorrelationTest.Empty
35: [ OK ] ManyAutocorrelationTest.Empty (1 ms)
35: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 11 tests from 2 test cases ran. (317 ms total)
35: [ PASSED ] 11 tests.
35/52 Test #35: CorrelationsTest .................... Passed 0.38 sec
test 36
Start 36: AnalysisDataUnitTests
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 69 tests from 14 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from AnalysisDataInitializationTest
36: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
36: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (1 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
36: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
36: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/0 (21 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
36: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/1 (25 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
36: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (3 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/2 (29 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
36: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (3 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/3 (28 ms total)
36:
36: [----------] 4 tests from AnalysisArrayDataTest
36: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
36: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisArrayDataTest.StorageWorks
36: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
36: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
36: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
36: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
36:
36: [----------] 6 tests from AverageModuleTest
36: [ RUN ] AverageModuleTest.BasicTest
36: [ OK ] AverageModuleTest.BasicTest (4 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipointData
36: [ OK ] AverageModuleTest.HandlesMultipointData (4 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
36: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
36: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
36: [ OK ] AverageModuleTest.HandlesDataSetAveraging (6 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeXAxis
36: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
36: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
36: [----------] 6 tests from AverageModuleTest (29 ms total)
36:
36: [----------] 2 tests from FrameAverageModuleTest
36: [ RUN ] FrameAverageModuleTest.BasicTest
36: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
36: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
36: [----------] 2 tests from FrameAverageModuleTest (10 ms total)
36:
36: [----------] 7 tests from AnalysisHistogramSettingsTest
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
36: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
36:
36: [----------] 2 tests from SimpleHistogramModuleTest
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (7 ms)
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
36: [----------] 2 tests from SimpleHistogramModuleTest (14 ms total)
36:
36: [----------] 3 tests from WeightedHistogramModuleTest
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
36: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
36: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (7 ms)
36: [----------] 3 tests from WeightedHistogramModuleTest (23 ms total)
36:
36: [----------] 3 tests from BinAverageModuleTest
36: [ RUN ] BinAverageModuleTest.ComputesCorrectly
36: [ OK ] BinAverageModuleTest.ComputesCorrectly (5 ms)
36: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
36: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
36: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 3 tests from BinAverageModuleTest (17 ms total)
36:
36: [----------] 4 tests from AbstractAverageHistogramTest
36: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
36: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (9 ms)
36: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
36: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms)
36: [----------] 4 tests from AbstractAverageHistogramTest (29 ms total)
36:
36: [----------] 3 tests from LifetimeModuleTest
36: [ RUN ] LifetimeModuleTest.BasicTest
36: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
36: [ RUN ] LifetimeModuleTest.CumulativeTest
36: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
36: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
36: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (5 ms)
36: [----------] 3 tests from LifetimeModuleTest (13 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 69 tests from 14 test cases ran. (247 ms total)
36: [ PASSED ] 69 tests.
36/52 Test #36: AnalysisDataUnitTests ............... Passed 0.32 sec
test 37
Start 37: CoordinateIOTests
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 64 tests from 19 test cases.
37: [----------] Global test environment set-up.
37: [----------] 1 test from OutputSelectorDeathTest
37: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (139 ms)
37: [----------] 1 test from OutputSelectorDeathTest (139 ms total)
37:
37: [----------] 5 tests from TrajectoryFrameWriterTest
37: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (22 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (43 ms)
37: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
37: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
37: [----------] 5 tests from TrajectoryFrameWriterTest (111 ms total)
37:
37: [----------] 5 tests from OutputAdapterContainer
37: [ RUN ] OutputAdapterContainer.MakeEmpty
37: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
37: [ RUN ] OutputAdapterContainer.AddAdapter
37: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectBadAdapter
37: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
37: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
37: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
37: [----------] 5 tests from OutputAdapterContainer (0 ms total)
37:
37: [----------] 5 tests from FlagTest
37: [ RUN ] FlagTest.CanSetSimpleFlag
37: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
37: [ RUN ] FlagTest.CanAddNewBox
37: [ OK ] FlagTest.CanAddNewBox (0 ms)
37: [ RUN ] FlagTest.SetsImplicitPrecisionChange
37: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitStartTimeChange
37: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitTimeStepChange
37: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
37: [----------] 5 tests from FlagTest (2 ms total)
37:
37: [----------] 5 tests from SetAtomsTest
37: [ RUN ] SetAtomsTest.RemovesExistingAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.RemovesExistingAtoms (22 ms)
37: [ RUN ] SetAtomsTest.AddsNewAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.AddsNewAtoms (21 ms)
37: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (21 ms)
37: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (22 ms)
37: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (21 ms)
37: [----------] 5 tests from SetAtomsTest (109 ms total)
37:
37: [----------] 2 tests from SetBothTimeTest
37: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
37: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
37: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
37: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
37: [----------] 2 tests from SetBothTimeTest (0 ms total)
37:
37: [----------] 2 tests from SetStartTimeTest
37: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
37: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
37: [ RUN ] SetStartTimeTest.WorksWithZeroStart
37: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
37: [----------] 2 tests from SetStartTimeTest (0 ms total)
37:
37: [----------] 1 test from SetTimeStepTest
37: [ RUN ] SetTimeStepTest.SetTimeStepWorks
37: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
37: [----------] 1 test from SetTimeStepTest (0 ms total)
37:
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (21 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (22 ms)
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (131 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (21 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (22 ms)
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (65 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total)
37:
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (45 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (44 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (45 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (44 ms)
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (178 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (21 ms)
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (65 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (21 ms)
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (43 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (1 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (22 ms)
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (44 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
37:
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (21 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (21 ms)
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput (86 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 64 tests from 19 test cases ran. (977 ms total)
37: [ PASSED ] 64 tests.
37/52 Test #37: CoordinateIOTests ................... Passed 1.05 sec
test 38
Start 38: TrajectoryAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 80 tests from 16 test cases.
38: [----------] Global test environment set-up.
38: [----------] 5 tests from ClustsizeTest
38: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 2, cmax: 4, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (16 ms)
38: [ RUN ] ClustsizeTest.NoMolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 1, cmax: 6, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (13 ms)
38: [ RUN ] ClustsizeTest.MolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (16 ms)
38: [ RUN ] ClustsizeTest.MolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 1, cmax: 6, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (15 ms)
38: [ RUN ] ClustsizeTest.MolCSize
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolCSize (15 ms)
38: [----------] 5 tests from ClustsizeTest (77 ms total)
38:
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (5 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (17 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (16 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (44 ms total)
38:
38: [----------] 11 tests from AngleModuleTest
38: [ RUN ] AngleModuleTest.ComputesSimpleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesSimpleAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesDihedrals
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesDihedrals (18 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPairAngles (17 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (17 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
38: Reading frames from gro file 'Test system for different angles', 33 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (19 ms)
38: [ RUN ] AngleModuleTest.ComputesMultipleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesMultipleAngles (18 ms)
38: [ RUN ] AngleModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesDynamicSelections (18 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (18 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (18 ms)
38: [----------] 11 tests from AngleModuleTest (198 ms total)
38:
38: [----------] 4 tests from ConvertTrjModuleTest
38: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (57 ms)
38: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (63 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (9 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (9 ms)
38: [----------] 4 tests from ConvertTrjModuleTest (139 ms total)
38:
38: [----------] 3 tests from DistanceModuleTest
38: [ RUN ] DistanceModuleTest.ComputesDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: [ OK ] DistanceModuleTest.ComputesDistances (21 ms)
38: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
38: Number of samples: 4
38: Average distance: 1.81066 nm
38: Standard deviation: 0.79289 nm
38: [ OK ] DistanceModuleTest.ComputesMultipleDistances (34 ms)
38: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2 and res_cog x < 2.8:
38: Number of samples: 3
38: Average distance: 1.72076 nm
38: Standard deviation: 1.24839 nm
38: [ OK ] DistanceModuleTest.HandlesDynamicSelections (23 ms)
38: [----------] 3 tests from DistanceModuleTest (80 ms total)
38:
38: [----------] 2 tests from ExtractClusterModuleTest
38: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
38: trr version: GMX_trn_file (single precision)
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (27 ms)
38: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (17 ms)
38: [----------] 2 tests from ExtractClusterModuleTest (44 ms total)
38:
38: [----------] 2 tests from FreeVolumeModuleTest
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for 40 particles. These were set to zero.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 13
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.02 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
38: Fractional free volume 0.194 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (694 ms)
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 17
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.48 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
38: Fractional free volume 0.200 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (690 ms)
38: [----------] 2 tests from FreeVolumeModuleTest (1384 ms total)
38:
38: [----------] 7 tests from PairDistanceModuleTest
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistances (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (17 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (17 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (17 ms)
38: [----------] 7 tests from PairDistanceModuleTest (123 ms total)
38:
38: [----------] 5 tests from RdfModuleTest
38: [ RUN ] RdfModuleTest.BasicTest
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.BasicTest (153 ms)
38: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
38: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (99 ms)
38: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (150 ms)
38: [ RUN ] RdfModuleTest.CalculatesSurf
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesSurf (90 ms)
38: [ RUN ] RdfModuleTest.CalculatesXY
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesXY (173 ms)
38: [----------] 5 tests from RdfModuleTest (668 ms total)
38:
38: [----------] 5 tests from SasaModuleTest
38: [ RUN ] SasaModuleTest.BasicTest
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.BasicTest (79 ms)
38: [ RUN ] SasaModuleTest.HandlesSelectedResidues
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesSelectedResidues (47 ms)
38: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (41 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (56 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (54 ms)
38: [----------] 5 tests from SasaModuleTest (288 ms total)
38:
38: [----------] 8 tests from SelectModuleTest
38: [ RUN ] SelectModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.BasicTest (32 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (24 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (23 ms)
38: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (23 ms)
38: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (24 ms)
38: [ RUN ] SelectModuleTest.NormalizesSizes
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.NormalizesSizes (16 ms)
38: [ RUN ] SelectModuleTest.WritesResidueNumbers
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueNumbers (16 ms)
38: [ RUN ] SelectModuleTest.WritesResidueIndices
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueIndices (16 ms)
38: [----------] 8 tests from SelectModuleTest (178 ms total)
38:
38: [----------] 10 tests from SurfaceAreaTest
38: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
38: [ OK ] SurfaceAreaTest.ComputesSinglePoint (1 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
38: [ OK ] SurfaceAreaTest.ComputesTwoPoints (6 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
38: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (7 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints12
38: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints32
38: [ OK ] SurfaceAreaTest.SurfacePoints32 (2 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints42
38: [ OK ] SurfaceAreaTest.SurfacePoints42 (2 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints122
38: [ OK ] SurfaceAreaTest.SurfacePoints122 (6 ms)
38: [ RUN ] SurfaceAreaTest.Computes100Points
38: [ OK ] SurfaceAreaTest.Computes100Points (4 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (14 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (16 ms)
38: [----------] 10 tests from SurfaceAreaTest (62 ms total)
38:
38: [----------] 4 tests from TopologyInformation
38: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
38: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (1 ms)
38: [ RUN ] TopologyInformation.WorksWithGroFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithGroFile (22 ms)
38: [ RUN ] TopologyInformation.WorksWithPdbFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithPdbFile (23 ms)
38: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: For a correct single-point energy evaluation with nsteps = 0, use
38: continuation = yes to avoid constraining the input coordinates.
38:
38: Setting the LD random seed to 1005478330
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
38:
38: NOTE 2 [file lysozyme.top, line 1465]:
38: System has non-zero total charge: 2.000000
38: Total charge should normally be an integer. See
38: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
38: for discussion on how close it should be to an integer.
38:
38:
38:
38: Number of degrees of freedom in T-Coupling group rest is 465.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: NVE simulation with an initial temperature of zero: will use a Verlet
38: buffer of 10%. Check your energy drift!
38:
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
38: Analysing residue names:
38: There are: 10 Protein residues
38: Analysing Protein...
38: This run will generate roughly 0 Mb of data
38: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (4445 ms)
38: [----------] 4 tests from TopologyInformation (4491 ms total)
38:
38: [----------] 4 tests from TrajectoryModuleTest
38: [ RUN ] TrajectoryModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.BasicTest (19 ms)
38: [ RUN ] TrajectoryModuleTest.PlotsXOnly
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.PlotsXOnly (19 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (18 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoForces
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoForces (18 ms)
38: [----------] 4 tests from TrajectoryModuleTest (75 ms total)
38:
38: [----------] 5 tests from UnionFinderTest
38: [ RUN ] UnionFinderTest.WorksEmpty
38: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
38: [ RUN ] UnionFinderTest.BasicMerges
38: [ OK ] UnionFinderTest.BasicMerges (1 ms)
38: [ RUN ] UnionFinderTest.LargerMerges
38: [ OK ] UnionFinderTest.LargerMerges (0 ms)
38: [ RUN ] UnionFinderTest.LongRightMerge
38: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
38: [ RUN ] UnionFinderTest.LongLeftMerge
38: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
38: [----------] 5 tests from UnionFinderTest (1 ms total)
38:
38: [----------] 1 test from MappedUnionFinderTest
38: [ RUN ] MappedUnionFinderTest.BasicMerges
38: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
38: [----------] 1 test from MappedUnionFinderTest (0 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 80 tests from 16 test cases ran. (7853 ms total)
38: [ PASSED ] 80 tests.
38/52 Test #38: TrajectoryAnalysisUnitTests ......... Passed 7.94 sec
test 39
Start 39: EnergyAnalysisUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 7 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 1 test from DhdlTest
39: [ RUN ] DhdlTest.ExtractDhdl
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
39: Note: file tpx version 110, software tpx version 119
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
39:
39:
39: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
39: [ OK ] DhdlTest.ExtractDhdl (121 ms)
39: [----------] 1 test from DhdlTest (124 ms total)
39:
39: [----------] 1 test from OriresTest
39: [ RUN ] OriresTest.ExtractOrires
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
39: Note: file tpx version 111, software tpx version 119
39: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
39: End your selection with 0
39: Selecting all 7 orientation restraints
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
39: [ OK ] OriresTest.ExtractOrires (73 ms)
39: [----------] 1 test from OriresTest (74 ms total)
39:
39: [----------] 3 tests from EnergyTest
39: [ RUN ] EnergyTest.ExtractEnergy
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: [ OK ] EnergyTest.ExtractEnergy (20 ms)
39: [ RUN ] EnergyTest.ExtractEnergyByNumber
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Pres. DC -268.49 3 8.52175 13.2804 (bar)
39: [ OK ] EnergyTest.ExtractEnergyByNumber (15 ms)
39: [ RUN ] EnergyTest.ExtractEnergyMixed
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: [ OK ] EnergyTest.ExtractEnergyMixed (16 ms)
39: [----------] 3 tests from EnergyTest (55 ms total)
39:
39: [----------] 2 tests from ViscosityTest
39: [ RUN ] ViscosityTest.EinsteinViscosity
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosity (37 ms)
39: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosityIntegral (42 ms)
39: [----------] 2 tests from ViscosityTest (80 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 7 tests from 4 test cases ran. (335 ms total)
39: [ PASSED ] 7 tests.
39/52 Test #39: EnergyAnalysisUnitTests ............. Passed 0.40 sec
test 40
Start 40: ToolUnitTests
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 18 tests from 4 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from DumpTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -327257755
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] DumpTest.WorksWithTpr
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
40: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
40: inputrec:
40: integrator = md
40: tinit = 0
40: dt = 0.001
40: nsteps = 0
40: init-step = 0
40: simulation-part = 1
40: comm-mode = Linear
40: nstcomm = 100
40: bd-fric = 0
40: ld-seed = -327257755
40: emtol = 10
40: emstep = 0.01
40: niter = 20
40: fcstep = 0
40: nstcgsteep = 1000
40: nbfgscorr = 10
40: rtpi = 0.05
40: nstxout = 0
40: nstvout = 0
40: nstfout = 0
40: nstlog = 1000
40: nstcalcenergy = 100
40: nstenergy = 1000
40: nstxout-compressed = 0
40: compressed-x-precision = 1000
40: cutoff-scheme = Verlet
40: nstlist = 10
40: pbc = xyz
40: periodic-molecules = false
40: verlet-buffer-tolerance = -1
40: rlist = 1.1
40: coulombtype = Cut-off
40: coulomb-modifier = Potential-shift
40: rcoulomb-switch = 0
40: rcoulomb = 1
40: epsilon-r = 1
40: epsilon-rf = inf
40: vdw-type = Cut-off
40: vdw-modifier = Potential-shift
40: rvdw-switch = 0
40: rvdw = 1
40: DispCorr = No
40: table-extension = 1
40: fourierspacing = 0.12
40: fourier-nx = 0
40: fourier-ny = 0
40: fourier-nz = 0
40: pme-order = 4
40: ewald-rtol = 1e-05
40: ewald-rtol-lj = 0.001
40: lj-pme-comb-rule = Geometric
40: ewald-geometry = 0
40: epsilon-surface = 0
40: tcoupl = No
40: nsttcouple = -1
40: nh-chain-length = 0
40: print-nose-hoover-chain-variables = false
40: pcoupl = No
40: pcoupltype = Isotropic
40: nstpcouple = -1
40: tau-p = 1
40: compressibility (3x3):
40: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p (3x3):
40: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: refcoord-scaling = No
40: posres-com (3):
40: posres-com[0]= 0.00000e+00
40: posres-com[1]= 0.00000e+00
40: posres-com[2]= 0.00000e+00
40: posres-comB (3):
40: posres-comB[0]= 0.00000e+00
40: posres-comB[1]= 0.00000e+00
40: posres-comB[2]= 0.00000e+00
40: QMMM = false
40: QMconstraints = 0
40: QMMMscheme = 0
40: MMChargeScaleFactor = 1
40: qm-opts:
40: ngQM = 0
40: constraint-algorithm = Lincs
40: continuation = false
40: Shake-SOR = false
40: shake-tol = 0.0001
40: lincs-order = 4
40: lincs-iter = 1
40: lincs-warnangle = 30
40: nwall = 0
40: wall-type = 9-3
40: wall-r-linpot = -1
40: wall-atomtype[0] = -1
40: wall-atomtype[1] = -1
40: wall-density[0] = 0
40: wall-density[1] = 0
40: wall-ewald-zfac = 3
40: pull = false
40: awh = false
40: rotation = false
40: interactiveMD = false
40: disre = No
40: disre-weighting = Conservative
40: disre-mixed = false
40: dr-fc = 1000
40: dr-tau = 0
40: nstdisreout = 100
40: orire-fc = 0
40: orire-tau = 0
40: nstorireout = 100
40: free-energy = no
40: cos-acceleration = 0
40: deform (3x3):
40: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: simulated-tempering = false
40: swapcoords = no
40: userint1 = 0
40: userint2 = 0
40: userint3 = 0
40: userint4 = 0
40: userreal1 = 0
40: userreal2 = 0
40: userreal3 = 0
40: userreal4 = 0
40: applied-forces:
40: electric-field:
40: x:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: y:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: z:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: density-guided-simulation:
40: active = false
40: group = protein
40: similarity-measure = inner-product
40: atom-spreading-weight = unity
40: force-constant = 1e+09
40: gaussian-transform-spreading-width = 0.2
40: gaussian-transform-spreading-range-in-multiples-of-width = 4
40: reference-density-filename = reference.mrc
40: nst = 1
40: normalize-densities = true
40: adaptive-force-scaling = false
40: adaptive-force-scaling-time-constant = 4
40: grpopts:
40: nrdf: 465
40: ref-t: 0
40: tau-t: 0
40: annealing: No
40: annealing-npoints: 0
40: acc: 0 0 0
40: nfreeze: N N N
40: energygrp-flags[ 0]: 0
40: header:
40: bIr = present
40: bBox = present
40: bTop = present
40: bX = present
40: bV = present
40: bF = not present
40: natoms = 156
40: lambda = 0.000000e+00
40: buffer size = 70122
40: topology:
40: name="First 10 residues from 1AKI"
40: #atoms = 156
40: #molblock = 1
40: molblock (0):
40: moltype = 0 "Protein_chain_B"
40: #molecules = 1
40: #posres_xA = 0
40: #posres_xB = 0
40: bIntermolecularInteractions = false
40: ffparams:
40: atnr=10
40: ntypes=212
40: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
40: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
40: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
40: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
40: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
40: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
40: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
40: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
40: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
40: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
40: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
40: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
40: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
40: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
40: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
40: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
40: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
40: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
40: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
40: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
40: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
40: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
40: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
40: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
40: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
40: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
40: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
40: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
40: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
40: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
40: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
40: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
40: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
40: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
40: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
40: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
40: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
40: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
40: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
40: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
40: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
40: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
40: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
40: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
40: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
40: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
40: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
40: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
40: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
40: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
40: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
40: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
40: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
40: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
40: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
40: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
40: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
40: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
40: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
40: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
40: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
40: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
40: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
40: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
40: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
40: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
40: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
40: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
40: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
40: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
40: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
40: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
40: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
40: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
40: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
40: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
40: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
40: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
40: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
40: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
40: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
40: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
40: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
40: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
40: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
40: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
40: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
40: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
40: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
40: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
40: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
40: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
40: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
40: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
40: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
40: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
40: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
40: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
40: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
40: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
40: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
40: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
40: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
40: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
40: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
40: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
40: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
40: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
40: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
40: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
40: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
40: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
40: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
40: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
40: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
40: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
40: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
40: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
40: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
40: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
40: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
40: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
40: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
40: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
40: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
40: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
40: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
40: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
40: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
40: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
40: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
40: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
40: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
40: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
40: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
40: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
40: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
40: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
40: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
40: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
40: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
40: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
40: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
40: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
40: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
40: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
40: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
40: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
40: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
40: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
40: reppow = 12
40: fudgeQQ = 0.5
40: cmap
40: atomtypes:
40: atomtype[ 0]={atomnumber= 7}
40: atomtype[ 1]={atomnumber= 1}
40: atomtype[ 2]={atomnumber= 6}
40: atomtype[ 3]={atomnumber= 1}
40: atomtype[ 4]={atomnumber= 6}
40: atomtype[ 5]={atomnumber= 8}
40: atomtype[ 6]={atomnumber= 6}
40: atomtype[ 7]={atomnumber= 1}
40: atomtype[ 8]={atomnumber= 6}
40: atomtype[ 9]={atomnumber= 16}
40: moltype (0):
40: name="Protein_chain_B"
40: atoms:
40: atom (156):
40: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
40: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
40: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
40: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
40: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
40: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
40: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
40: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
40: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
40: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
40: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
40: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
40: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
40: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
40: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
40: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
40: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
40: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
40: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
40: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
40: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
40: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
40: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
40: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
40: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
40: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
40: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
40: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
40: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
40: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
40: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
40: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
40: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
40: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
40: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
40: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
40: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
40: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
40: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
40: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
40: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
40: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
40: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
40: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
40: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
40: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
40: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
40: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
40: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
40: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
40: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
40: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
40: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
40: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
40: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
40: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
40: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
40: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
40: atom (156):
40: atom[0]={name="N"}
40: atom[1]={name="H1"}
40: atom[2]={name="H2"}
40: atom[3]={name="H3"}
40: atom[4]={name="CA"}
40: atom[5]={name="HA"}
40: atom[6]={name="CB"}
40: atom[7]={name="HB1"}
40: atom[8]={name="HB2"}
40: atom[9]={name="CG"}
40: atom[10]={name="HG1"}
40: atom[11]={name="HG2"}
40: atom[12]={name="CD"}
40: atom[13]={name="HD1"}
40: atom[14]={name="HD2"}
40: atom[15]={name="CE"}
40: atom[16]={name="HE1"}
40: atom[17]={name="HE2"}
40: atom[18]={name="NZ"}
40: atom[19]={name="HZ1"}
40: atom[20]={name="HZ2"}
40: atom[21]={name="HZ3"}
40: atom[22]={name="C"}
40: atom[23]={name="O"}
40: atom[24]={name="N"}
40: atom[25]={name="H"}
40: atom[26]={name="CA"}
40: atom[27]={name="HA"}
40: atom[28]={name="CB"}
40: atom[29]={name="HB"}
40: atom[30]={name="CG1"}
40: atom[31]={name="HG11"}
40: atom[32]={name="HG12"}
40: atom[33]={name="HG13"}
40: atom[34]={name="CG2"}
40: atom[35]={name="HG21"}
40: atom[36]={name="HG22"}
40: atom[37]={name="HG23"}
40: atom[38]={name="C"}
40: atom[39]={name="O"}
40: atom[40]={name="N"}
40: atom[41]={name="H"}
40: atom[42]={name="CA"}
40: atom[43]={name="HA"}
40: atom[44]={name="CB"}
40: atom[45]={name="HB1"}
40: atom[46]={name="HB2"}
40: atom[47]={name="CG"}
40: atom[48]={name="CD1"}
40: atom[49]={name="HD1"}
40: atom[50]={name="CD2"}
40: atom[51]={name="HD2"}
40: atom[52]={name="CE1"}
40: atom[53]={name="HE1"}
40: atom[54]={name="CE2"}
40: atom[55]={name="HE2"}
40: atom[56]={name="CZ"}
40: atom[57]={name="HZ"}
40: atom[58]={name="C"}
40: atom[59]={name="O"}
40: atom[60]={name="N"}
40: atom[61]={name="H"}
40: atom[62]={name="CA"}
40: atom[63]={name="HA1"}
40: atom[64]={name="HA2"}
40: atom[65]={name="C"}
40: atom[66]={name="O"}
40: atom[67]={name="N"}
40: atom[68]={name="H"}
40: atom[69]={name="CA"}
40: atom[70]={name="HA"}
40: atom[71]={name="CB"}
40: atom[72]={name="HB1"}
40: atom[73]={name="HB2"}
40: atom[74]={name="CG"}
40: atom[75]={name="HG1"}
40: atom[76]={name="HG2"}
40: atom[77]={name="CD"}
40: atom[78]={name="HD1"}
40: atom[79]={name="HD2"}
40: atom[80]={name="NE"}
40: atom[81]={name="HE"}
40: atom[82]={name="CZ"}
40: atom[83]={name="NH1"}
40: atom[84]={name="HH11"}
40: atom[85]={name="HH12"}
40: atom[86]={name="NH2"}
40: atom[87]={name="HH21"}
40: atom[88]={name="HH22"}
40: atom[89]={name="C"}
40: atom[90]={name="O"}
40: atom[91]={name="N"}
40: atom[92]={name="H"}
40: atom[93]={name="CA"}
40: atom[94]={name="HA"}
40: atom[95]={name="CB"}
40: atom[96]={name="HB1"}
40: atom[97]={name="HB2"}
40: atom[98]={name="SG"}
40: atom[99]={name="HG"}
40: atom[100]={name="C"}
40: atom[101]={name="O"}
40: atom[102]={name="N"}
40: atom[103]={name="H"}
40: atom[104]={name="CA"}
40: atom[105]={name="HA"}
40: atom[106]={name="CB"}
40: atom[107]={name="HB1"}
40: atom[108]={name="HB2"}
40: atom[109]={name="CG"}
40: atom[110]={name="HG1"}
40: atom[111]={name="HG2"}
40: atom[112]={name="CD"}
40: atom[113]={name="OE1"}
40: atom[114]={name="OE2"}
40: atom[115]={name="C"}
40: atom[116]={name="O"}
40: atom[117]={name="N"}
40: atom[118]={name="H"}
40: atom[119]={name="CA"}
40: atom[120]={name="HA"}
40: atom[121]={name="CB"}
40: atom[122]={name="HB1"}
40: atom[123]={name="HB2"}
40: atom[124]={name="CG"}
40: atom[125]={name="HG"}
40: atom[126]={name="CD1"}
40: atom[127]={name="HD11"}
40: atom[128]={name="HD12"}
40: atom[129]={name="HD13"}
40: atom[130]={name="CD2"}
40: atom[131]={name="HD21"}
40: atom[132]={name="HD22"}
40: atom[133]={name="HD23"}
40: atom[134]={name="C"}
40: atom[135]={name="O"}
40: atom[136]={name="N"}
40: atom[137]={name="H"}
40: atom[138]={name="CA"}
40: atom[139]={name="HA"}
40: atom[140]={name="CB"}
40: atom[141]={name="HB1"}
40: atom[142]={name="HB2"}
40: atom[143]={name="HB3"}
40: atom[144]={name="C"}
40: atom[145]={name="O"}
40: atom[146]={name="N"}
40: atom[147]={name="H"}
40: atom[148]={name="CA"}
40: atom[149]={name="HA"}
40: atom[150]={name="CB"}
40: atom[151]={name="HB1"}
40: atom[152]={name="HB2"}
40: atom[153]={name="HB3"}
40: atom[154]={name="C"}
40: atom[155]={name="O"}
40: type (156):
40: type[0]={name="opls_287",nameB="opls_287"}
40: type[1]={name="opls_290",nameB="opls_290"}
40: type[2]={name="opls_290",nameB="opls_290"}
40: type[3]={name="opls_290",nameB="opls_290"}
40: type[4]={name="opls_293B",nameB="opls_293B"}
40: type[5]={name="opls_140",nameB="opls_140"}
40: type[6]={name="opls_136",nameB="opls_136"}
40: type[7]={name="opls_140",nameB="opls_140"}
40: type[8]={name="opls_140",nameB="opls_140"}
40: type[9]={name="opls_136",nameB="opls_136"}
40: type[10]={name="opls_140",nameB="opls_140"}
40: type[11]={name="opls_140",nameB="opls_140"}
40: type[12]={name="opls_136",nameB="opls_136"}
40: type[13]={name="opls_140",nameB="opls_140"}
40: type[14]={name="opls_140",nameB="opls_140"}
40: type[15]={name="opls_292",nameB="opls_292"}
40: type[16]={name="opls_140",nameB="opls_140"}
40: type[17]={name="opls_140",nameB="opls_140"}
40: type[18]={name="opls_287",nameB="opls_287"}
40: type[19]={name="opls_290",nameB="opls_290"}
40: type[20]={name="opls_290",nameB="opls_290"}
40: type[21]={name="opls_290",nameB="opls_290"}
40: type[22]={name="opls_235",nameB="opls_235"}
40: type[23]={name="opls_236",nameB="opls_236"}
40: type[24]={name="opls_238",nameB="opls_238"}
40: type[25]={name="opls_241",nameB="opls_241"}
40: type[26]={name="opls_224B",nameB="opls_224B"}
40: type[27]={name="opls_140",nameB="opls_140"}
40: type[28]={name="opls_137",nameB="opls_137"}
40: type[29]={name="opls_140",nameB="opls_140"}
40: type[30]={name="opls_135",nameB="opls_135"}
40: type[31]={name="opls_140",nameB="opls_140"}
40: type[32]={name="opls_140",nameB="opls_140"}
40: type[33]={name="opls_140",nameB="opls_140"}
40: type[34]={name="opls_135",nameB="opls_135"}
40: type[35]={name="opls_140",nameB="opls_140"}
40: type[36]={name="opls_140",nameB="opls_140"}
40: type[37]={name="opls_140",nameB="opls_140"}
40: type[38]={name="opls_235",nameB="opls_235"}
40: type[39]={name="opls_236",nameB="opls_236"}
40: type[40]={name="opls_238",nameB="opls_238"}
40: type[41]={name="opls_241",nameB="opls_241"}
40: type[42]={name="opls_224B",nameB="opls_224B"}
40: type[43]={name="opls_140",nameB="opls_140"}
40: type[44]={name="opls_149",nameB="opls_149"}
40: type[45]={name="opls_140",nameB="opls_140"}
40: type[46]={name="opls_140",nameB="opls_140"}
40: type[47]={name="opls_145",nameB="opls_145"}
40: type[48]={name="opls_145",nameB="opls_145"}
40: type[49]={name="opls_146",nameB="opls_146"}
40: type[50]={name="opls_145",nameB="opls_145"}
40: type[51]={name="opls_146",nameB="opls_146"}
40: type[52]={name="opls_145",nameB="opls_145"}
40: type[53]={name="opls_146",nameB="opls_146"}
40: type[54]={name="opls_145",nameB="opls_145"}
40: type[55]={name="opls_146",nameB="opls_146"}
40: type[56]={name="opls_145",nameB="opls_145"}
40: type[57]={name="opls_146",nameB="opls_146"}
40: type[58]={name="opls_235",nameB="opls_235"}
40: type[59]={name="opls_236",nameB="opls_236"}
40: type[60]={name="opls_238",nameB="opls_238"}
40: type[61]={name="opls_241",nameB="opls_241"}
40: type[62]={name="opls_223B",nameB="opls_223B"}
40: type[63]={name="opls_140",nameB="opls_140"}
40: type[64]={name="opls_140",nameB="opls_140"}
40: type[65]={name="opls_235",nameB="opls_235"}
40: type[66]={name="opls_236",nameB="opls_236"}
40: type[67]={name="opls_238",nameB="opls_238"}
40: type[68]={name="opls_241",nameB="opls_241"}
40: type[69]={name="opls_224B",nameB="opls_224B"}
40: type[70]={name="opls_140",nameB="opls_140"}
40: type[71]={name="opls_136",nameB="opls_136"}
40: type[72]={name="opls_140",nameB="opls_140"}
40: type[73]={name="opls_140",nameB="opls_140"}
40: type[74]={name="opls_308",nameB="opls_308"}
40: type[75]={name="opls_140",nameB="opls_140"}
40: type[76]={name="opls_140",nameB="opls_140"}
40: type[77]={name="opls_307",nameB="opls_307"}
40: type[78]={name="opls_140",nameB="opls_140"}
40: type[79]={name="opls_140",nameB="opls_140"}
40: type[80]={name="opls_303",nameB="opls_303"}
40: type[81]={name="opls_304",nameB="opls_304"}
40: type[82]={name="opls_302",nameB="opls_302"}
40: type[83]={name="opls_300",nameB="opls_300"}
40: type[84]={name="opls_301",nameB="opls_301"}
40: type[85]={name="opls_301",nameB="opls_301"}
40: type[86]={name="opls_300",nameB="opls_300"}
40: type[87]={name="opls_301",nameB="opls_301"}
40: type[88]={name="opls_301",nameB="opls_301"}
40: type[89]={name="opls_235",nameB="opls_235"}
40: type[90]={name="opls_236",nameB="opls_236"}
40: type[91]={name="opls_238",nameB="opls_238"}
40: type[92]={name="opls_241",nameB="opls_241"}
40: type[93]={name="opls_224B",nameB="opls_224B"}
40: type[94]={name="opls_140",nameB="opls_140"}
40: type[95]={name="opls_206",nameB="opls_206"}
40: type[96]={name="opls_140",nameB="opls_140"}
40: type[97]={name="opls_140",nameB="opls_140"}
40: type[98]={name="opls_200",nameB="opls_200"}
40: type[99]={name="opls_204",nameB="opls_204"}
40: type[100]={name="opls_235",nameB="opls_235"}
40: type[101]={name="opls_236",nameB="opls_236"}
40: type[102]={name="opls_238",nameB="opls_238"}
40: type[103]={name="opls_241",nameB="opls_241"}
40: type[104]={name="opls_224B",nameB="opls_224B"}
40: type[105]={name="opls_140",nameB="opls_140"}
40: type[106]={name="opls_136",nameB="opls_136"}
40: type[107]={name="opls_140",nameB="opls_140"}
40: type[108]={name="opls_140",nameB="opls_140"}
40: type[109]={name="opls_274",nameB="opls_274"}
40: type[110]={name="opls_140",nameB="opls_140"}
40: type[111]={name="opls_140",nameB="opls_140"}
40: type[112]={name="opls_271",nameB="opls_271"}
40: type[113]={name="opls_272",nameB="opls_272"}
40: type[114]={name="opls_272",nameB="opls_272"}
40: type[115]={name="opls_235",nameB="opls_235"}
40: type[116]={name="opls_236",nameB="opls_236"}
40: type[117]={name="opls_238",nameB="opls_238"}
40: type[118]={name="opls_241",nameB="opls_241"}
40: type[119]={name="opls_224B",nameB="opls_224B"}
40: type[120]={name="opls_140",nameB="opls_140"}
40: type[121]={name="opls_136",nameB="opls_136"}
40: type[122]={name="opls_140",nameB="opls_140"}
40: type[123]={name="opls_140",nameB="opls_140"}
40: type[124]={name="opls_137",nameB="opls_137"}
40: type[125]={name="opls_140",nameB="opls_140"}
40: type[126]={name="opls_135",nameB="opls_135"}
40: type[127]={name="opls_140",nameB="opls_140"}
40: type[128]={name="opls_140",nameB="opls_140"}
40: type[129]={name="opls_140",nameB="opls_140"}
40: type[130]={name="opls_135",nameB="opls_135"}
40: type[131]={name="opls_140",nameB="opls_140"}
40: type[132]={name="opls_140",nameB="opls_140"}
40: type[133]={name="opls_140",nameB="opls_140"}
40: type[134]={name="opls_235",nameB="opls_235"}
40: type[135]={name="opls_236",nameB="opls_236"}
40: type[136]={name="opls_238",nameB="opls_238"}
40: type[137]={name="opls_241",nameB="opls_241"}
40: type[138]={name="opls_224B",nameB="opls_224B"}
40: type[139]={name="opls_140",nameB="opls_140"}
40: type[140]={name="opls_135",nameB="opls_135"}
40: type[141]={name="opls_140",nameB="opls_140"}
40: type[142]={name="opls_140",nameB="opls_140"}
40: type[143]={name="opls_140",nameB="opls_140"}
40: type[144]={name="opls_235",nameB="opls_235"}
40: type[145]={name="opls_236",nameB="opls_236"}
40: type[146]={name="opls_238",nameB="opls_238"}
40: type[147]={name="opls_241",nameB="opls_241"}
40: type[148]={name="opls_224B",nameB="opls_224B"}
40: type[149]={name="opls_140",nameB="opls_140"}
40: type[150]={name="opls_135",nameB="opls_135"}
40: type[151]={name="opls_140",nameB="opls_140"}
40: type[152]={name="opls_140",nameB="opls_140"}
40: type[153]={name="opls_140",nameB="opls_140"}
40: type[154]={name="opls_235",nameB="opls_235"}
40: type[155]={name="opls_236",nameB="opls_236"}
40: residue (10):
40: residue[0]={name="LYS", nr=1, ic=' '}
40: residue[1]={name="VAL", nr=2, ic=' '}
40: residue[2]={name="PHE", nr=3, ic=' '}
40: residue[3]={name="GLY", nr=4, ic=' '}
40: residue[4]={name="ARG", nr=5, ic=' '}
40: residue[5]={name="CYS", nr=6, ic=' '}
40: residue[6]={name="GLU", nr=7, ic=' '}
40: residue[7]={name="LEU", nr=8, ic=' '}
40: residue[8]={name="ALA", nr=9, ic=' '}
40: residue[9]={name="ALA", nr=10, ic=' '}
40: excls:
40: nr=156
40: nra=1828
40: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
40: 23, 24, 25, 26}
40: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
40: 14, 15, 22, 23, 24}
40: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
40: 16, 17, 18, 22}
40: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
40: 17, 18, 19, 20, 21}
40: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
40: 19, 20, 21}
40: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
40: 25, 26, 27, 28, 38}
40: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
40: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
40: 30, 34, 38, 39, 40}
40: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
40: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
40: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
40: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40}
40: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
40: 34, 35, 36, 37, 38, 39, 40}
40: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40, 41, 42, 43, 44, 58}
40: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
40: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
40: 45, 46, 47, 58, 59, 60}
40: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
40: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
40: 48, 50, 58, 59, 60, 61, 62}
40: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60}
40: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
40: 50, 51, 52, 54, 58, 59, 60}
40: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
40: 52, 53, 54, 55, 56, 58}
40: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
40: 54, 56, 57}
40: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
40: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
40: 55, 56, 57}
40: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
40: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
40: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
40: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
40: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
40: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60, 61, 62, 63, 64, 65}
40: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
40: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
40: 65, 66, 67}
40: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
40: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
40: 68, 69}
40: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
40: 70, 71, 89}
40: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
40: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
40: 72, 73, 74, 89, 90, 91}
40: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
40: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
40: 75, 76, 77, 89, 90, 91, 92, 93}
40: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
40: 91}
40: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
40: 77, 78, 79, 80, 89, 90, 91}
40: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
40: 79, 80, 81, 82, 89}
40: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
40: 81, 82, 83, 86}
40: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
40: 84, 85, 86, 87, 88}
40: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
40: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
40: 86, 87, 88}
40: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
40: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
40: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
40: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
40: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
40: 90, 91, 92, 93, 94, 95, 100}
40: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
40: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
40: 95, 96, 97, 98, 100, 101, 102}
40: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
40: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
40: 98, 99, 100, 101, 102, 103, 104}
40: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102}
40: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
40: 100, 101, 102}
40: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
40: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102, 103, 104, 105, 106, 115}
40: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
40: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
40: 105, 106, 107, 108, 109, 115, 116, 117}
40: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
40: 115}
40: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
40: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
40: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117}
40: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 110, 111, 112, 113, 114, 115, 116, 117}
40: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 113, 114, 115}
40: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
40: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
40: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117, 118, 119, 120, 121, 134}
40: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119}
40: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119, 120, 121, 122, 123, 124, 134, 135, 136}
40: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
40: 134}
40: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
40: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
40: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136}
40: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
40: 136}
40: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 127, 128, 129, 130, 131, 132, 133, 134}
40: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136, 137, 138, 139, 140, 144}
40: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138}
40: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138, 139, 140, 141, 142, 143, 144, 145, 146}
40: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
40: 144}
40: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
40: 141, 142, 143, 144, 145, 146, 147, 148}
40: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146, 147, 148, 149, 150, 154}
40: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148}
40: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148, 149, 150, 151, 152, 153, 154, 155}
40: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
40: 154}
40: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
40: 151, 152, 153, 154, 155}
40: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
40: Bond:
40: nr: 468
40: iatoms:
40: 0 type=100 (BONDS) 0 1
40: 1 type=100 (BONDS) 0 2
40: 2 type=100 (BONDS) 0 3
40: 3 type=101 (BONDS) 0 4
40: 4 type=102 (BONDS) 4 5
40: 5 type=103 (BONDS) 4 6
40: 6 type=104 (BONDS) 4 22
40: 7 type=102 (BONDS) 6 7
40: 8 type=102 (BONDS) 6 8
40: 9 type=103 (BONDS) 6 9
40: 10 type=102 (BONDS) 9 10
40: 11 type=102 (BONDS) 9 11
40: 12 type=103 (BONDS) 9 12
40: 13 type=102 (BONDS) 12 13
40: 14 type=102 (BONDS) 12 14
40: 15 type=103 (BONDS) 12 15
40: 16 type=102 (BONDS) 15 16
40: 17 type=102 (BONDS) 15 17
40: 18 type=101 (BONDS) 15 18
40: 19 type=100 (BONDS) 18 19
40: 20 type=100 (BONDS) 18 20
40: 21 type=100 (BONDS) 18 21
40: 22 type=105 (BONDS) 22 23
40: 23 type=106 (BONDS) 22 24
40: 24 type=100 (BONDS) 24 25
40: 25 type=107 (BONDS) 24 26
40: 26 type=102 (BONDS) 26 27
40: 27 type=103 (BONDS) 26 28
40: 28 type=104 (BONDS) 26 38
40: 29 type=102 (BONDS) 28 29
40: 30 type=103 (BONDS) 28 30
40: 31 type=103 (BONDS) 28 34
40: 32 type=102 (BONDS) 30 31
40: 33 type=102 (BONDS) 30 32
40: 34 type=102 (BONDS) 30 33
40: 35 type=102 (BONDS) 34 35
40: 36 type=102 (BONDS) 34 36
40: 37 type=102 (BONDS) 34 37
40: 38 type=105 (BONDS) 38 39
40: 39 type=106 (BONDS) 38 40
40: 40 type=100 (BONDS) 40 41
40: 41 type=107 (BONDS) 40 42
40: 42 type=102 (BONDS) 42 43
40: 43 type=103 (BONDS) 42 44
40: 44 type=104 (BONDS) 42 58
40: 45 type=102 (BONDS) 44 45
40: 46 type=102 (BONDS) 44 46
40: 47 type=108 (BONDS) 44 47
40: 48 type=109 (BONDS) 47 48
40: 49 type=109 (BONDS) 47 50
40: 50 type=110 (BONDS) 48 49
40: 51 type=109 (BONDS) 48 52
40: 52 type=110 (BONDS) 50 51
40: 53 type=109 (BONDS) 50 54
40: 54 type=110 (BONDS) 52 53
40: 55 type=109 (BONDS) 52 56
40: 56 type=110 (BONDS) 54 55
40: 57 type=109 (BONDS) 54 56
40: 58 type=110 (BONDS) 56 57
40: 59 type=105 (BONDS) 58 59
40: 60 type=106 (BONDS) 58 60
40: 61 type=100 (BONDS) 60 61
40: 62 type=107 (BONDS) 60 62
40: 63 type=102 (BONDS) 62 63
40: 64 type=102 (BONDS) 62 64
40: 65 type=104 (BONDS) 62 65
40: 66 type=105 (BONDS) 65 66
40: 67 type=106 (BONDS) 65 67
40: 68 type=100 (BONDS) 67 68
40: 69 type=107 (BONDS) 67 69
40: 70 type=102 (BONDS) 69 70
40: 71 type=103 (BONDS) 69 71
40: 72 type=104 (BONDS) 69 89
40: 73 type=102 (BONDS) 71 72
40: 74 type=102 (BONDS) 71 73
40: 75 type=103 (BONDS) 71 74
40: 76 type=102 (BONDS) 74 75
40: 77 type=102 (BONDS) 74 76
40: 78 type=103 (BONDS) 74 77
40: 79 type=102 (BONDS) 77 78
40: 80 type=102 (BONDS) 77 79
40: 81 type=111 (BONDS) 77 80
40: 82 type=100 (BONDS) 80 81
40: 83 type=112 (BONDS) 80 82
40: 84 type=112 (BONDS) 82 83
40: 85 type=112 (BONDS) 82 86
40: 86 type=100 (BONDS) 83 84
40: 87 type=100 (BONDS) 83 85
40: 88 type=100 (BONDS) 86 87
40: 89 type=100 (BONDS) 86 88
40: 90 type=105 (BONDS) 89 90
40: 91 type=106 (BONDS) 89 91
40: 92 type=100 (BONDS) 91 92
40: 93 type=107 (BONDS) 91 93
40: 94 type=102 (BONDS) 93 94
40: 95 type=103 (BONDS) 93 95
40: 96 type=104 (BONDS) 93 100
40: 97 type=102 (BONDS) 95 96
40: 98 type=102 (BONDS) 95 97
40: 99 type=113 (BONDS) 95 98
40: 100 type=114 (BONDS) 98 99
40: 101 type=105 (BONDS) 100 101
40: 102 type=106 (BONDS) 100 102
40: 103 type=100 (BONDS) 102 103
40: 104 type=107 (BONDS) 102 104
40: 105 type=102 (BONDS) 104 105
40: 106 type=103 (BONDS) 104 106
40: 107 type=104 (BONDS) 104 115
40: 108 type=102 (BONDS) 106 107
40: 109 type=102 (BONDS) 106 108
40: 110 type=103 (BONDS) 106 109
40: 111 type=102 (BONDS) 109 110
40: 112 type=102 (BONDS) 109 111
40: 113 type=104 (BONDS) 109 112
40: 114 type=115 (BONDS) 112 113
40: 115 type=115 (BONDS) 112 114
40: 116 type=105 (BONDS) 115 116
40: 117 type=106 (BONDS) 115 117
40: 118 type=100 (BONDS) 117 118
40: 119 type=107 (BONDS) 117 119
40: 120 type=102 (BONDS) 119 120
40: 121 type=103 (BONDS) 119 121
40: 122 type=104 (BONDS) 119 134
40: 123 type=102 (BONDS) 121 122
40: 124 type=102 (BONDS) 121 123
40: 125 type=103 (BONDS) 121 124
40: 126 type=102 (BONDS) 124 125
40: 127 type=103 (BONDS) 124 126
40: 128 type=103 (BONDS) 124 130
40: 129 type=102 (BONDS) 126 127
40: 130 type=102 (BONDS) 126 128
40: 131 type=102 (BONDS) 126 129
40: 132 type=102 (BONDS) 130 131
40: 133 type=102 (BONDS) 130 132
40: 134 type=102 (BONDS) 130 133
40: 135 type=105 (BONDS) 134 135
40: 136 type=106 (BONDS) 134 136
40: 137 type=100 (BONDS) 136 137
40: 138 type=107 (BONDS) 136 138
40: 139 type=102 (BONDS) 138 139
40: 140 type=103 (BONDS) 138 140
40: 141 type=104 (BONDS) 138 144
40: 142 type=102 (BONDS) 140 141
40: 143 type=102 (BONDS) 140 142
40: 144 type=102 (BONDS) 140 143
40: 145 type=105 (BONDS) 144 145
40: 146 type=106 (BONDS) 144 146
40: 147 type=100 (BONDS) 146 147
40: 148 type=107 (BONDS) 146 148
40: 149 type=102 (BONDS) 148 149
40: 150 type=103 (BONDS) 148 150
40: 151 type=104 (BONDS) 148 154
40: 152 type=102 (BONDS) 150 151
40: 153 type=102 (BONDS) 150 152
40: 154 type=102 (BONDS) 150 153
40: 155 type=105 (BONDS) 154 155
40: G96Bond:
40: nr: 0
40: Morse:
40: nr: 0
40: Cubic Bonds:
40: nr: 0
40: Connect Bonds:
40: nr: 0
40: Harmonic Pot.:
40: nr: 0
40: FENE Bonds:
40: nr: 0
40: Tab. Bonds:
40: nr: 0
40: Tab. Bonds NC:
40: nr: 0
40: Restraint Pot.:
40: nr: 0
40: Angle:
40: nr: 1124
40: iatoms:
40: 0 type=116 (ANGLES) 1 0 2
40: 1 type=116 (ANGLES) 1 0 3
40: 2 type=116 (ANGLES) 1 0 4
40: 3 type=116 (ANGLES) 2 0 3
40: 4 type=116 (ANGLES) 2 0 4
40: 5 type=116 (ANGLES) 3 0 4
40: 6 type=116 (ANGLES) 0 4 5
40: 7 type=117 (ANGLES) 0 4 6
40: 8 type=117 (ANGLES) 0 4 22
40: 9 type=118 (ANGLES) 5 4 6
40: 10 type=116 (ANGLES) 5 4 22
40: 11 type=119 (ANGLES) 6 4 22
40: 12 type=118 (ANGLES) 4 6 7
40: 13 type=118 (ANGLES) 4 6 8
40: 14 type=120 (ANGLES) 4 6 9
40: 15 type=121 (ANGLES) 7 6 8
40: 16 type=118 (ANGLES) 7 6 9
40: 17 type=118 (ANGLES) 8 6 9
40: 18 type=118 (ANGLES) 6 9 10
40: 19 type=118 (ANGLES) 6 9 11
40: 20 type=120 (ANGLES) 6 9 12
40: 21 type=121 (ANGLES) 10 9 11
40: 22 type=118 (ANGLES) 10 9 12
40: 23 type=118 (ANGLES) 11 9 12
40: 24 type=118 (ANGLES) 9 12 13
40: 25 type=118 (ANGLES) 9 12 14
40: 26 type=120 (ANGLES) 9 12 15
40: 27 type=121 (ANGLES) 13 12 14
40: 28 type=118 (ANGLES) 13 12 15
40: 29 type=118 (ANGLES) 14 12 15
40: 30 type=118 (ANGLES) 12 15 16
40: 31 type=118 (ANGLES) 12 15 17
40: 32 type=117 (ANGLES) 12 15 18
40: 33 type=121 (ANGLES) 16 15 17
40: 34 type=116 (ANGLES) 16 15 18
40: 35 type=116 (ANGLES) 17 15 18
40: 36 type=116 (ANGLES) 15 18 19
40: 37 type=116 (ANGLES) 15 18 20
40: 38 type=116 (ANGLES) 15 18 21
40: 39 type=116 (ANGLES) 19 18 20
40: 40 type=116 (ANGLES) 19 18 21
40: 41 type=116 (ANGLES) 20 18 21
40: 42 type=122 (ANGLES) 4 22 23
40: 43 type=123 (ANGLES) 4 22 24
40: 44 type=124 (ANGLES) 23 22 24
40: 45 type=125 (ANGLES) 22 24 25
40: 46 type=126 (ANGLES) 22 24 26
40: 47 type=127 (ANGLES) 25 24 26
40: 48 type=116 (ANGLES) 24 26 27
40: 49 type=128 (ANGLES) 24 26 28
40: 50 type=129 (ANGLES) 24 26 38
40: 51 type=118 (ANGLES) 27 26 28
40: 52 type=116 (ANGLES) 27 26 38
40: 53 type=119 (ANGLES) 28 26 38
40: 54 type=118 (ANGLES) 26 28 29
40: 55 type=120 (ANGLES) 26 28 30
40: 56 type=120 (ANGLES) 26 28 34
40: 57 type=118 (ANGLES) 29 28 30
40: 58 type=118 (ANGLES) 29 28 34
40: 59 type=120 (ANGLES) 30 28 34
40: 60 type=118 (ANGLES) 28 30 31
40: 61 type=118 (ANGLES) 28 30 32
40: 62 type=118 (ANGLES) 28 30 33
40: 63 type=121 (ANGLES) 31 30 32
40: 64 type=121 (ANGLES) 31 30 33
40: 65 type=121 (ANGLES) 32 30 33
40: 66 type=118 (ANGLES) 28 34 35
40: 67 type=118 (ANGLES) 28 34 36
40: 68 type=118 (ANGLES) 28 34 37
40: 69 type=121 (ANGLES) 35 34 36
40: 70 type=121 (ANGLES) 35 34 37
40: 71 type=121 (ANGLES) 36 34 37
40: 72 type=122 (ANGLES) 26 38 39
40: 73 type=123 (ANGLES) 26 38 40
40: 74 type=124 (ANGLES) 39 38 40
40: 75 type=125 (ANGLES) 38 40 41
40: 76 type=126 (ANGLES) 38 40 42
40: 77 type=127 (ANGLES) 41 40 42
40: 78 type=116 (ANGLES) 40 42 43
40: 79 type=128 (ANGLES) 40 42 44
40: 80 type=129 (ANGLES) 40 42 58
40: 81 type=118 (ANGLES) 43 42 44
40: 82 type=116 (ANGLES) 43 42 58
40: 83 type=119 (ANGLES) 44 42 58
40: 84 type=118 (ANGLES) 42 44 45
40: 85 type=118 (ANGLES) 42 44 46
40: 86 type=130 (ANGLES) 42 44 47
40: 87 type=121 (ANGLES) 45 44 46
40: 88 type=116 (ANGLES) 45 44 47
40: 89 type=116 (ANGLES) 46 44 47
40: 90 type=131 (ANGLES) 44 47 48
40: 91 type=131 (ANGLES) 44 47 50
40: 92 type=132 (ANGLES) 48 47 50
40: 93 type=133 (ANGLES) 47 48 49
40: 94 type=132 (ANGLES) 47 48 52
40: 95 type=133 (ANGLES) 49 48 52
40: 96 type=133 (ANGLES) 47 50 51
40: 97 type=132 (ANGLES) 47 50 54
40: 98 type=133 (ANGLES) 51 50 54
40: 99 type=133 (ANGLES) 48 52 53
40: 100 type=132 (ANGLES) 48 52 56
40: 101 type=133 (ANGLES) 53 52 56
40: 102 type=133 (ANGLES) 50 54 55
40: 103 type=132 (ANGLES) 50 54 56
40: 104 type=133 (ANGLES) 55 54 56
40: 105 type=132 (ANGLES) 52 56 54
40: 106 type=133 (ANGLES) 52 56 57
40: 107 type=133 (ANGLES) 54 56 57
40: 108 type=122 (ANGLES) 42 58 59
40: 109 type=123 (ANGLES) 42 58 60
40: 110 type=124 (ANGLES) 59 58 60
40: 111 type=125 (ANGLES) 58 60 61
40: 112 type=126 (ANGLES) 58 60 62
40: 113 type=127 (ANGLES) 61 60 62
40: 114 type=116 (ANGLES) 60 62 63
40: 115 type=116 (ANGLES) 60 62 64
40: 116 type=129 (ANGLES) 60 62 65
40: 117 type=121 (ANGLES) 63 62 64
40: 118 type=116 (ANGLES) 63 62 65
40: 119 type=116 (ANGLES) 64 62 65
40: 120 type=122 (ANGLES) 62 65 66
40: 121 type=123 (ANGLES) 62 65 67
40: 122 type=124 (ANGLES) 66 65 67
40: 123 type=125 (ANGLES) 65 67 68
40: 124 type=126 (ANGLES) 65 67 69
40: 125 type=127 (ANGLES) 68 67 69
40: 126 type=116 (ANGLES) 67 69 70
40: 127 type=128 (ANGLES) 67 69 71
40: 128 type=129 (ANGLES) 67 69 89
40: 129 type=118 (ANGLES) 70 69 71
40: 130 type=116 (ANGLES) 70 69 89
40: 131 type=119 (ANGLES) 71 69 89
40: 132 type=118 (ANGLES) 69 71 72
40: 133 type=118 (ANGLES) 69 71 73
40: 134 type=120 (ANGLES) 69 71 74
40: 135 type=121 (ANGLES) 72 71 73
40: 136 type=118 (ANGLES) 72 71 74
40: 137 type=118 (ANGLES) 73 71 74
40: 138 type=118 (ANGLES) 71 74 75
40: 139 type=118 (ANGLES) 71 74 76
40: 140 type=120 (ANGLES) 71 74 77
40: 141 type=121 (ANGLES) 75 74 76
40: 142 type=118 (ANGLES) 75 74 77
40: 143 type=118 (ANGLES) 76 74 77
40: 144 type=118 (ANGLES) 74 77 78
40: 145 type=118 (ANGLES) 74 77 79
40: 146 type=117 (ANGLES) 74 77 80
40: 147 type=121 (ANGLES) 78 77 79
40: 148 type=116 (ANGLES) 78 77 80
40: 149 type=116 (ANGLES) 79 77 80
40: 150 type=134 (ANGLES) 77 80 81
40: 151 type=135 (ANGLES) 77 80 82
40: 152 type=133 (ANGLES) 81 80 82
40: 153 type=131 (ANGLES) 80 82 83
40: 154 type=131 (ANGLES) 80 82 86
40: 155 type=131 (ANGLES) 83 82 86
40: 156 type=133 (ANGLES) 82 83 84
40: 157 type=133 (ANGLES) 82 83 85
40: 158 type=133 (ANGLES) 84 83 85
40: 159 type=133 (ANGLES) 82 86 87
40: 160 type=133 (ANGLES) 82 86 88
40: 161 type=133 (ANGLES) 87 86 88
40: 162 type=122 (ANGLES) 69 89 90
40: 163 type=123 (ANGLES) 69 89 91
40: 164 type=124 (ANGLES) 90 89 91
40: 165 type=125 (ANGLES) 89 91 92
40: 166 type=126 (ANGLES) 89 91 93
40: 167 type=127 (ANGLES) 92 91 93
40: 168 type=116 (ANGLES) 91 93 94
40: 169 type=128 (ANGLES) 91 93 95
40: 170 type=129 (ANGLES) 91 93 100
40: 171 type=118 (ANGLES) 94 93 95
40: 172 type=116 (ANGLES) 94 93 100
40: 173 type=119 (ANGLES) 95 93 100
40: 174 type=118 (ANGLES) 93 95 96
40: 175 type=118 (ANGLES) 93 95 97
40: 176 type=136 (ANGLES) 93 95 98
40: 177 type=121 (ANGLES) 96 95 97
40: 178 type=116 (ANGLES) 96 95 98
40: 179 type=116 (ANGLES) 97 95 98
40: 180 type=137 (ANGLES) 95 98 99
40: 181 type=122 (ANGLES) 93 100 101
40: 182 type=123 (ANGLES) 93 100 102
40: 183 type=124 (ANGLES) 101 100 102
40: 184 type=125 (ANGLES) 100 102 103
40: 185 type=126 (ANGLES) 100 102 104
40: 186 type=127 (ANGLES) 103 102 104
40: 187 type=116 (ANGLES) 102 104 105
40: 188 type=128 (ANGLES) 102 104 106
40: 189 type=129 (ANGLES) 102 104 115
40: 190 type=118 (ANGLES) 105 104 106
40: 191 type=116 (ANGLES) 105 104 115
40: 192 type=119 (ANGLES) 106 104 115
40: 193 type=118 (ANGLES) 104 106 107
40: 194 type=118 (ANGLES) 104 106 108
40: 195 type=120 (ANGLES) 104 106 109
40: 196 type=121 (ANGLES) 107 106 108
40: 197 type=118 (ANGLES) 107 106 109
40: 198 type=118 (ANGLES) 108 106 109
40: 199 type=118 (ANGLES) 106 109 110
40: 200 type=118 (ANGLES) 106 109 111
40: 201 type=119 (ANGLES) 106 109 112
40: 202 type=121 (ANGLES) 110 109 111
40: 203 type=116 (ANGLES) 110 109 112
40: 204 type=116 (ANGLES) 111 109 112
40: 205 type=138 (ANGLES) 109 112 113
40: 206 type=138 (ANGLES) 109 112 114
40: 207 type=139 (ANGLES) 113 112 114
40: 208 type=122 (ANGLES) 104 115 116
40: 209 type=123 (ANGLES) 104 115 117
40: 210 type=124 (ANGLES) 116 115 117
40: 211 type=125 (ANGLES) 115 117 118
40: 212 type=126 (ANGLES) 115 117 119
40: 213 type=127 (ANGLES) 118 117 119
40: 214 type=116 (ANGLES) 117 119 120
40: 215 type=128 (ANGLES) 117 119 121
40: 216 type=129 (ANGLES) 117 119 134
40: 217 type=118 (ANGLES) 120 119 121
40: 218 type=116 (ANGLES) 120 119 134
40: 219 type=119 (ANGLES) 121 119 134
40: 220 type=118 (ANGLES) 119 121 122
40: 221 type=118 (ANGLES) 119 121 123
40: 222 type=120 (ANGLES) 119 121 124
40: 223 type=121 (ANGLES) 122 121 123
40: 224 type=118 (ANGLES) 122 121 124
40: 225 type=118 (ANGLES) 123 121 124
40: 226 type=118 (ANGLES) 121 124 125
40: 227 type=120 (ANGLES) 121 124 126
40: 228 type=120 (ANGLES) 121 124 130
40: 229 type=118 (ANGLES) 125 124 126
40: 230 type=118 (ANGLES) 125 124 130
40: 231 type=120 (ANGLES) 126 124 130
40: 232 type=118 (ANGLES) 124 126 127
40: 233 type=118 (ANGLES) 124 126 128
40: 234 type=118 (ANGLES) 124 126 129
40: 235 type=121 (ANGLES) 127 126 128
40: 236 type=121 (ANGLES) 127 126 129
40: 237 type=121 (ANGLES) 128 126 129
40: 238 type=118 (ANGLES) 124 130 131
40: 239 type=118 (ANGLES) 124 130 132
40: 240 type=118 (ANGLES) 124 130 133
40: 241 type=121 (ANGLES) 131 130 132
40: 242 type=121 (ANGLES) 131 130 133
40: 243 type=121 (ANGLES) 132 130 133
40: 244 type=122 (ANGLES) 119 134 135
40: 245 type=123 (ANGLES) 119 134 136
40: 246 type=124 (ANGLES) 135 134 136
40: 247 type=125 (ANGLES) 134 136 137
40: 248 type=126 (ANGLES) 134 136 138
40: 249 type=127 (ANGLES) 137 136 138
40: 250 type=116 (ANGLES) 136 138 139
40: 251 type=128 (ANGLES) 136 138 140
40: 252 type=129 (ANGLES) 136 138 144
40: 253 type=118 (ANGLES) 139 138 140
40: 254 type=116 (ANGLES) 139 138 144
40: 255 type=119 (ANGLES) 140 138 144
40: 256 type=118 (ANGLES) 138 140 141
40: 257 type=118 (ANGLES) 138 140 142
40: 258 type=118 (ANGLES) 138 140 143
40: 259 type=121 (ANGLES) 141 140 142
40: 260 type=121 (ANGLES) 141 140 143
40: 261 type=121 (ANGLES) 142 140 143
40: 262 type=122 (ANGLES) 138 144 145
40: 263 type=123 (ANGLES) 138 144 146
40: 264 type=124 (ANGLES) 145 144 146
40: 265 type=125 (ANGLES) 144 146 147
40: 266 type=126 (ANGLES) 144 146 148
40: 267 type=127 (ANGLES) 147 146 148
40: 268 type=116 (ANGLES) 146 148 149
40: 269 type=128 (ANGLES) 146 148 150
40: 270 type=129 (ANGLES) 146 148 154
40: 271 type=118 (ANGLES) 149 148 150
40: 272 type=116 (ANGLES) 149 148 154
40: 273 type=119 (ANGLES) 150 148 154
40: 274 type=118 (ANGLES) 148 150 151
40: 275 type=118 (ANGLES) 148 150 152
40: 276 type=118 (ANGLES) 148 150 153
40: 277 type=121 (ANGLES) 151 150 152
40: 278 type=121 (ANGLES) 151 150 153
40: 279 type=121 (ANGLES) 152 150 153
40: 280 type=122 (ANGLES) 148 154 155
40: G96Angle:
40: nr: 0
40: Restricted Angles:
40: nr: 0
40: Lin. Angle:
40: nr: 0
40: Bond-Cross:
40: nr: 0
40: BA-Cross:
40: nr: 0
40: U-B:
40: nr: 0
40: Quartic Angles:
40: nr: 0
40: Tab. Angles:
40: nr: 0
40: Proper Dih.:
40: nr: 145
40: iatoms:
40: 0 type=140 (PDIHS) 4 24 22 23
40: 1 type=141 (PDIHS) 22 26 24 25
40: 2 type=140 (PDIHS) 26 40 38 39
40: 3 type=141 (PDIHS) 38 42 40 41
40: 4 type=140 (PDIHS) 42 60 58 59
40: 5 type=142 (PDIHS) 44 47 50 48
40: 6 type=142 (PDIHS) 47 52 48 49
40: 7 type=142 (PDIHS) 47 54 50 51
40: 8 type=142 (PDIHS) 48 56 52 53
40: 9 type=142 (PDIHS) 50 56 54 55
40: 10 type=142 (PDIHS) 52 54 56 57
40: 11 type=141 (PDIHS) 58 62 60 61
40: 12 type=140 (PDIHS) 62 67 65 66
40: 13 type=141 (PDIHS) 65 69 67 68
40: 14 type=140 (PDIHS) 69 91 89 90
40: 15 type=141 (PDIHS) 77 82 80 81
40: 16 type=140 (PDIHS) 80 83 82 86
40: 17 type=141 (PDIHS) 82 84 83 85
40: 18 type=141 (PDIHS) 82 87 86 88
40: 19 type=141 (PDIHS) 89 93 91 92
40: 20 type=140 (PDIHS) 93 102 100 101
40: 21 type=141 (PDIHS) 100 104 102 103
40: 22 type=140 (PDIHS) 104 117 115 116
40: 23 type=140 (PDIHS) 109 113 112 114
40: 24 type=141 (PDIHS) 115 119 117 118
40: 25 type=140 (PDIHS) 119 136 134 135
40: 26 type=141 (PDIHS) 134 138 136 137
40: 27 type=140 (PDIHS) 138 146 144 145
40: 28 type=141 (PDIHS) 144 148 146 147
40: Ryckaert-Bell.:
40: nr: 1565
40: iatoms:
40: 0 type=143 (RBDIHS) 1 0 4 5
40: 1 type=144 (RBDIHS) 1 0 4 6
40: 2 type=144 (RBDIHS) 1 0 4 22
40: 3 type=143 (RBDIHS) 2 0 4 5
40: 4 type=144 (RBDIHS) 2 0 4 6
40: 5 type=144 (RBDIHS) 2 0 4 22
40: 6 type=143 (RBDIHS) 3 0 4 5
40: 7 type=144 (RBDIHS) 3 0 4 6
40: 8 type=144 (RBDIHS) 3 0 4 22
40: 9 type=145 (RBDIHS) 0 4 6 9
40: 10 type=146 (RBDIHS) 22 4 6 9
40: 11 type=147 (RBDIHS) 0 4 6 7
40: 12 type=147 (RBDIHS) 0 4 6 8
40: 13 type=148 (RBDIHS) 5 4 6 7
40: 14 type=148 (RBDIHS) 5 4 6 8
40: 15 type=148 (RBDIHS) 5 4 6 9
40: 16 type=149 (RBDIHS) 22 4 6 7
40: 17 type=149 (RBDIHS) 22 4 6 8
40: 18 type=150 (RBDIHS) 0 4 22 24
40: 19 type=151 (RBDIHS) 6 4 22 24
40: 20 type=148 (RBDIHS) 4 6 9 10
40: 21 type=148 (RBDIHS) 4 6 9 11
40: 22 type=152 (RBDIHS) 4 6 9 12
40: 23 type=148 (RBDIHS) 7 6 9 10
40: 24 type=148 (RBDIHS) 7 6 9 11
40: 25 type=148 (RBDIHS) 7 6 9 12
40: 26 type=148 (RBDIHS) 8 6 9 10
40: 27 type=148 (RBDIHS) 8 6 9 11
40: 28 type=148 (RBDIHS) 8 6 9 12
40: 29 type=148 (RBDIHS) 6 9 12 13
40: 30 type=148 (RBDIHS) 6 9 12 14
40: 31 type=152 (RBDIHS) 6 9 12 15
40: 32 type=148 (RBDIHS) 10 9 12 13
40: 33 type=148 (RBDIHS) 10 9 12 14
40: 34 type=148 (RBDIHS) 10 9 12 15
40: 35 type=148 (RBDIHS) 11 9 12 13
40: 36 type=148 (RBDIHS) 11 9 12 14
40: 37 type=148 (RBDIHS) 11 9 12 15
40: 38 type=148 (RBDIHS) 9 12 15 16
40: 39 type=148 (RBDIHS) 9 12 15 17
40: 40 type=153 (RBDIHS) 9 12 15 18
40: 41 type=148 (RBDIHS) 13 12 15 16
40: 42 type=148 (RBDIHS) 13 12 15 17
40: 43 type=154 (RBDIHS) 13 12 15 18
40: 44 type=148 (RBDIHS) 14 12 15 16
40: 45 type=148 (RBDIHS) 14 12 15 17
40: 46 type=154 (RBDIHS) 14 12 15 18
40: 47 type=144 (RBDIHS) 12 15 18 19
40: 48 type=144 (RBDIHS) 12 15 18 20
40: 49 type=144 (RBDIHS) 12 15 18 21
40: 50 type=143 (RBDIHS) 16 15 18 19
40: 51 type=143 (RBDIHS) 16 15 18 20
40: 52 type=143 (RBDIHS) 16 15 18 21
40: 53 type=143 (RBDIHS) 17 15 18 19
40: 54 type=143 (RBDIHS) 17 15 18 20
40: 55 type=143 (RBDIHS) 17 15 18 21
40: 56 type=155 (RBDIHS) 4 22 24 25
40: 57 type=156 (RBDIHS) 4 22 24 26
40: 58 type=155 (RBDIHS) 23 22 24 25
40: 59 type=157 (RBDIHS) 23 22 24 26
40: 60 type=158 (RBDIHS) 22 24 26 28
40: 61 type=159 (RBDIHS) 22 24 26 38
40: 62 type=160 (RBDIHS) 24 26 28 30
40: 63 type=160 (RBDIHS) 24 26 28 34
40: 64 type=161 (RBDIHS) 38 26 28 30
40: 65 type=161 (RBDIHS) 38 26 28 34
40: 66 type=147 (RBDIHS) 24 26 28 29
40: 67 type=148 (RBDIHS) 27 26 28 29
40: 68 type=148 (RBDIHS) 27 26 28 30
40: 69 type=148 (RBDIHS) 27 26 28 34
40: 70 type=149 (RBDIHS) 38 26 28 29
40: 71 type=150 (RBDIHS) 24 26 38 40
40: 72 type=151 (RBDIHS) 28 26 38 40
40: 73 type=148 (RBDIHS) 26 28 30 31
40: 74 type=148 (RBDIHS) 26 28 30 32
40: 75 type=148 (RBDIHS) 26 28 30 33
40: 76 type=148 (RBDIHS) 29 28 30 31
40: 77 type=148 (RBDIHS) 29 28 30 32
40: 78 type=148 (RBDIHS) 29 28 30 33
40: 79 type=148 (RBDIHS) 34 28 30 31
40: 80 type=148 (RBDIHS) 34 28 30 32
40: 81 type=148 (RBDIHS) 34 28 30 33
40: 82 type=148 (RBDIHS) 26 28 34 35
40: 83 type=148 (RBDIHS) 26 28 34 36
40: 84 type=148 (RBDIHS) 26 28 34 37
40: 85 type=148 (RBDIHS) 29 28 34 35
40: 86 type=148 (RBDIHS) 29 28 34 36
40: 87 type=148 (RBDIHS) 29 28 34 37
40: 88 type=148 (RBDIHS) 30 28 34 35
40: 89 type=148 (RBDIHS) 30 28 34 36
40: 90 type=148 (RBDIHS) 30 28 34 37
40: 91 type=155 (RBDIHS) 26 38 40 41
40: 92 type=156 (RBDIHS) 26 38 40 42
40: 93 type=155 (RBDIHS) 39 38 40 41
40: 94 type=157 (RBDIHS) 39 38 40 42
40: 95 type=158 (RBDIHS) 38 40 42 44
40: 96 type=159 (RBDIHS) 38 40 42 58
40: 97 type=147 (RBDIHS) 40 42 44 45
40: 98 type=147 (RBDIHS) 40 42 44 46
40: 99 type=162 (RBDIHS) 40 42 44 47
40: 100 type=148 (RBDIHS) 43 42 44 45
40: 101 type=148 (RBDIHS) 43 42 44 46
40: 102 type=163 (RBDIHS) 43 42 44 47
40: 103 type=149 (RBDIHS) 58 42 44 45
40: 104 type=149 (RBDIHS) 58 42 44 46
40: 105 type=164 (RBDIHS) 58 42 44 47
40: 106 type=150 (RBDIHS) 40 42 58 60
40: 107 type=151 (RBDIHS) 44 42 58 60
40: 108 type=165 (RBDIHS) 44 47 48 49
40: 109 type=165 (RBDIHS) 44 47 48 52
40: 110 type=165 (RBDIHS) 50 47 48 49
40: 111 type=165 (RBDIHS) 50 47 48 52
40: 112 type=165 (RBDIHS) 44 47 50 51
40: 113 type=165 (RBDIHS) 44 47 50 54
40: 114 type=165 (RBDIHS) 48 47 50 51
40: 115 type=165 (RBDIHS) 48 47 50 54
40: 116 type=165 (RBDIHS) 47 48 52 53
40: 117 type=165 (RBDIHS) 47 48 52 56
40: 118 type=165 (RBDIHS) 49 48 52 53
40: 119 type=165 (RBDIHS) 49 48 52 56
40: 120 type=165 (RBDIHS) 47 50 54 55
40: 121 type=165 (RBDIHS) 47 50 54 56
40: 122 type=165 (RBDIHS) 51 50 54 55
40: 123 type=165 (RBDIHS) 51 50 54 56
40: 124 type=165 (RBDIHS) 48 52 56 54
40: 125 type=165 (RBDIHS) 48 52 56 57
40: 126 type=165 (RBDIHS) 53 52 56 54
40: 127 type=165 (RBDIHS) 53 52 56 57
40: 128 type=165 (RBDIHS) 50 54 56 52
40: 129 type=165 (RBDIHS) 50 54 56 57
40: 130 type=165 (RBDIHS) 55 54 56 52
40: 131 type=165 (RBDIHS) 55 54 56 57
40: 132 type=155 (RBDIHS) 42 58 60 61
40: 133 type=156 (RBDIHS) 42 58 60 62
40: 134 type=155 (RBDIHS) 59 58 60 61
40: 135 type=157 (RBDIHS) 59 58 60 62
40: 136 type=159 (RBDIHS) 58 60 62 65
40: 137 type=150 (RBDIHS) 60 62 65 67
40: 138 type=155 (RBDIHS) 62 65 67 68
40: 139 type=156 (RBDIHS) 62 65 67 69
40: 140 type=155 (RBDIHS) 66 65 67 68
40: 141 type=157 (RBDIHS) 66 65 67 69
40: 142 type=158 (RBDIHS) 65 67 69 71
40: 143 type=159 (RBDIHS) 65 67 69 89
40: 144 type=166 (RBDIHS) 67 69 71 74
40: 145 type=167 (RBDIHS) 89 69 71 74
40: 146 type=147 (RBDIHS) 67 69 71 72
40: 147 type=147 (RBDIHS) 67 69 71 73
40: 148 type=148 (RBDIHS) 70 69 71 72
40: 149 type=148 (RBDIHS) 70 69 71 73
40: 150 type=148 (RBDIHS) 70 69 71 74
40: 151 type=149 (RBDIHS) 89 69 71 72
40: 152 type=149 (RBDIHS) 89 69 71 73
40: 153 type=150 (RBDIHS) 67 69 89 91
40: 154 type=151 (RBDIHS) 71 69 89 91
40: 155 type=148 (RBDIHS) 69 71 74 75
40: 156 type=148 (RBDIHS) 69 71 74 76
40: 157 type=152 (RBDIHS) 69 71 74 77
40: 158 type=148 (RBDIHS) 72 71 74 75
40: 159 type=148 (RBDIHS) 72 71 74 76
40: 160 type=148 (RBDIHS) 72 71 74 77
40: 161 type=148 (RBDIHS) 73 71 74 75
40: 162 type=148 (RBDIHS) 73 71 74 76
40: 163 type=148 (RBDIHS) 73 71 74 77
40: 164 type=148 (RBDIHS) 71 74 77 78
40: 165 type=148 (RBDIHS) 71 74 77 79
40: 166 type=153 (RBDIHS) 71 74 77 80
40: 167 type=148 (RBDIHS) 75 74 77 78
40: 168 type=148 (RBDIHS) 75 74 77 79
40: 169 type=168 (RBDIHS) 75 74 77 80
40: 170 type=148 (RBDIHS) 76 74 77 78
40: 171 type=148 (RBDIHS) 76 74 77 79
40: 172 type=168 (RBDIHS) 76 74 77 80
40: 173 type=169 (RBDIHS) 74 77 80 81
40: 174 type=170 (RBDIHS) 74 77 80 82
40: 175 type=171 (RBDIHS) 78 77 80 82
40: 176 type=171 (RBDIHS) 79 77 80 82
40: 177 type=172 (RBDIHS) 77 80 82 83
40: 178 type=172 (RBDIHS) 77 80 82 86
40: 179 type=173 (RBDIHS) 81 80 82 83
40: 180 type=173 (RBDIHS) 81 80 82 86
40: 181 type=173 (RBDIHS) 80 82 83 84
40: 182 type=173 (RBDIHS) 80 82 83 85
40: 183 type=173 (RBDIHS) 86 82 83 84
40: 184 type=173 (RBDIHS) 86 82 83 85
40: 185 type=173 (RBDIHS) 80 82 86 87
40: 186 type=173 (RBDIHS) 80 82 86 88
40: 187 type=173 (RBDIHS) 83 82 86 87
40: 188 type=173 (RBDIHS) 83 82 86 88
40: 189 type=155 (RBDIHS) 69 89 91 92
40: 190 type=156 (RBDIHS) 69 89 91 93
40: 191 type=155 (RBDIHS) 90 89 91 92
40: 192 type=157 (RBDIHS) 90 89 91 93
40: 193 type=158 (RBDIHS) 89 91 93 95
40: 194 type=159 (RBDIHS) 89 91 93 100
40: 195 type=174 (RBDIHS) 91 93 95 98
40: 196 type=175 (RBDIHS) 100 93 95 98
40: 197 type=147 (RBDIHS) 91 93 95 96
40: 198 type=147 (RBDIHS) 91 93 95 97
40: 199 type=148 (RBDIHS) 94 93 95 96
40: 200 type=148 (RBDIHS) 94 93 95 97
40: 201 type=176 (RBDIHS) 94 93 95 98
40: 202 type=149 (RBDIHS) 100 93 95 96
40: 203 type=149 (RBDIHS) 100 93 95 97
40: 204 type=150 (RBDIHS) 91 93 100 102
40: 205 type=151 (RBDIHS) 95 93 100 102
40: 206 type=177 (RBDIHS) 93 95 98 99
40: 207 type=178 (RBDIHS) 96 95 98 99
40: 208 type=178 (RBDIHS) 97 95 98 99
40: 209 type=155 (RBDIHS) 93 100 102 103
40: 210 type=156 (RBDIHS) 93 100 102 104
40: 211 type=155 (RBDIHS) 101 100 102 103
40: 212 type=157 (RBDIHS) 101 100 102 104
40: 213 type=158 (RBDIHS) 100 102 104 106
40: 214 type=159 (RBDIHS) 100 102 104 115
40: 215 type=179 (RBDIHS) 102 104 106 109
40: 216 type=180 (RBDIHS) 115 104 106 109
40: 217 type=147 (RBDIHS) 102 104 106 107
40: 218 type=147 (RBDIHS) 102 104 106 108
40: 219 type=148 (RBDIHS) 105 104 106 107
40: 220 type=148 (RBDIHS) 105 104 106 108
40: 221 type=148 (RBDIHS) 105 104 106 109
40: 222 type=149 (RBDIHS) 115 104 106 107
40: 223 type=149 (RBDIHS) 115 104 106 108
40: 224 type=150 (RBDIHS) 102 104 115 117
40: 225 type=151 (RBDIHS) 106 104 115 117
40: 226 type=148 (RBDIHS) 104 106 109 110
40: 227 type=148 (RBDIHS) 104 106 109 111
40: 228 type=181 (RBDIHS) 104 106 109 112
40: 229 type=148 (RBDIHS) 107 106 109 110
40: 230 type=148 (RBDIHS) 107 106 109 111
40: 231 type=182 (RBDIHS) 107 106 109 112
40: 232 type=148 (RBDIHS) 108 106 109 110
40: 233 type=148 (RBDIHS) 108 106 109 111
40: 234 type=182 (RBDIHS) 108 106 109 112
40: 235 type=183 (RBDIHS) 106 109 112 113
40: 236 type=183 (RBDIHS) 106 109 112 114
40: 237 type=155 (RBDIHS) 104 115 117 118
40: 238 type=156 (RBDIHS) 104 115 117 119
40: 239 type=155 (RBDIHS) 116 115 117 118
40: 240 type=157 (RBDIHS) 116 115 117 119
40: 241 type=158 (RBDIHS) 115 117 119 121
40: 242 type=159 (RBDIHS) 115 117 119 134
40: 243 type=184 (RBDIHS) 117 119 121 124
40: 244 type=185 (RBDIHS) 134 119 121 124
40: 245 type=147 (RBDIHS) 117 119 121 122
40: 246 type=147 (RBDIHS) 117 119 121 123
40: 247 type=148 (RBDIHS) 120 119 121 122
40: 248 type=148 (RBDIHS) 120 119 121 123
40: 249 type=148 (RBDIHS) 120 119 121 124
40: 250 type=149 (RBDIHS) 134 119 121 122
40: 251 type=149 (RBDIHS) 134 119 121 123
40: 252 type=150 (RBDIHS) 117 119 134 136
40: 253 type=151 (RBDIHS) 121 119 134 136
40: 254 type=148 (RBDIHS) 119 121 124 125
40: 255 type=152 (RBDIHS) 119 121 124 126
40: 256 type=152 (RBDIHS) 119 121 124 130
40: 257 type=148 (RBDIHS) 122 121 124 125
40: 258 type=148 (RBDIHS) 122 121 124 126
40: 259 type=148 (RBDIHS) 122 121 124 130
40: 260 type=148 (RBDIHS) 123 121 124 125
40: 261 type=148 (RBDIHS) 123 121 124 126
40: 262 type=148 (RBDIHS) 123 121 124 130
40: 263 type=148 (RBDIHS) 121 124 126 127
40: 264 type=148 (RBDIHS) 121 124 126 128
40: 265 type=148 (RBDIHS) 121 124 126 129
40: 266 type=148 (RBDIHS) 125 124 126 127
40: 267 type=148 (RBDIHS) 125 124 126 128
40: 268 type=148 (RBDIHS) 125 124 126 129
40: 269 type=148 (RBDIHS) 130 124 126 127
40: 270 type=148 (RBDIHS) 130 124 126 128
40: 271 type=148 (RBDIHS) 130 124 126 129
40: 272 type=148 (RBDIHS) 121 124 130 131
40: 273 type=148 (RBDIHS) 121 124 130 132
40: 274 type=148 (RBDIHS) 121 124 130 133
40: 275 type=148 (RBDIHS) 125 124 130 131
40: 276 type=148 (RBDIHS) 125 124 130 132
40: 277 type=148 (RBDIHS) 125 124 130 133
40: 278 type=148 (RBDIHS) 126 124 130 131
40: 279 type=148 (RBDIHS) 126 124 130 132
40: 280 type=148 (RBDIHS) 126 124 130 133
40: 281 type=155 (RBDIHS) 119 134 136 137
40: 282 type=156 (RBDIHS) 119 134 136 138
40: 283 type=155 (RBDIHS) 135 134 136 137
40: 284 type=157 (RBDIHS) 135 134 136 138
40: 285 type=158 (RBDIHS) 134 136 138 140
40: 286 type=159 (RBDIHS) 134 136 138 144
40: 287 type=147 (RBDIHS) 136 138 140 141
40: 288 type=147 (RBDIHS) 136 138 140 142
40: 289 type=147 (RBDIHS) 136 138 140 143
40: 290 type=148 (RBDIHS) 139 138 140 141
40: 291 type=148 (RBDIHS) 139 138 140 142
40: 292 type=148 (RBDIHS) 139 138 140 143
40: 293 type=149 (RBDIHS) 144 138 140 141
40: 294 type=149 (RBDIHS) 144 138 140 142
40: 295 type=149 (RBDIHS) 144 138 140 143
40: 296 type=150 (RBDIHS) 136 138 144 146
40: 297 type=151 (RBDIHS) 140 138 144 146
40: 298 type=155 (RBDIHS) 138 144 146 147
40: 299 type=156 (RBDIHS) 138 144 146 148
40: 300 type=155 (RBDIHS) 145 144 146 147
40: 301 type=157 (RBDIHS) 145 144 146 148
40: 302 type=158 (RBDIHS) 144 146 148 150
40: 303 type=159 (RBDIHS) 144 146 148 154
40: 304 type=147 (RBDIHS) 146 148 150 151
40: 305 type=147 (RBDIHS) 146 148 150 152
40: 306 type=147 (RBDIHS) 146 148 150 153
40: 307 type=148 (RBDIHS) 149 148 150 151
40: 308 type=148 (RBDIHS) 149 148 150 152
40: 309 type=148 (RBDIHS) 149 148 150 153
40: 310 type=149 (RBDIHS) 154 148 150 151
40: 311 type=149 (RBDIHS) 154 148 150 152
40: 312 type=149 (RBDIHS) 154 148 150 153
40: Restricted Dih.:
40: nr: 0
40: CBT Dih.:
40: nr: 0
40: Fourier Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Tab. Dih.:
40: nr: 0
40: CMAP Dih.:
40: nr: 0
40: GB 1-2 Pol. (unused):
40: nr: 0
40: GB 1-3 Pol. (unused):
40: nr: 0
40: GB 1-4 Pol. (unused):
40: nr: 0
40: GB Polarization (unused):
40: nr: 0
40: Nonpolar Sol. (unused):
40: nr: 0
40: LJ-14:
40: nr: 1197
40: iatoms:
40: 0 type=186 (LJ14) 0 7
40: 1 type=186 (LJ14) 0 8
40: 2 type=187 (LJ14) 0 9
40: 3 type=188 (LJ14) 0 23
40: 4 type=189 (LJ14) 0 24
40: 5 type=190 (LJ14) 1 5
40: 6 type=190 (LJ14) 1 6
40: 7 type=190 (LJ14) 1 22
40: 8 type=190 (LJ14) 2 5
40: 9 type=190 (LJ14) 2 6
40: 10 type=190 (LJ14) 2 22
40: 11 type=190 (LJ14) 3 5
40: 12 type=190 (LJ14) 3 6
40: 13 type=190 (LJ14) 3 22
40: 14 type=191 (LJ14) 4 10
40: 15 type=191 (LJ14) 4 11
40: 16 type=192 (LJ14) 4 12
40: 17 type=190 (LJ14) 4 25
40: 18 type=192 (LJ14) 4 26
40: 19 type=193 (LJ14) 5 7
40: 20 type=193 (LJ14) 5 8
40: 21 type=191 (LJ14) 5 9
40: 22 type=194 (LJ14) 5 23
40: 23 type=186 (LJ14) 5 24
40: 24 type=191 (LJ14) 6 13
40: 25 type=191 (LJ14) 6 14
40: 26 type=192 (LJ14) 6 15
40: 27 type=195 (LJ14) 6 23
40: 28 type=187 (LJ14) 6 24
40: 29 type=193 (LJ14) 7 10
40: 30 type=193 (LJ14) 7 11
40: 31 type=191 (LJ14) 7 12
40: 32 type=196 (LJ14) 7 22
40: 33 type=193 (LJ14) 8 10
40: 34 type=193 (LJ14) 8 11
40: 35 type=191 (LJ14) 8 12
40: 36 type=196 (LJ14) 8 22
40: 37 type=191 (LJ14) 9 16
40: 38 type=191 (LJ14) 9 17
40: 39 type=187 (LJ14) 9 18
40: 40 type=197 (LJ14) 9 22
40: 41 type=193 (LJ14) 10 13
40: 42 type=193 (LJ14) 10 14
40: 43 type=191 (LJ14) 10 15
40: 44 type=193 (LJ14) 11 13
40: 45 type=193 (LJ14) 11 14
40: 46 type=191 (LJ14) 11 15
40: 47 type=190 (LJ14) 12 19
40: 48 type=190 (LJ14) 12 20
40: 49 type=190 (LJ14) 12 21
40: 50 type=193 (LJ14) 13 16
40: 51 type=193 (LJ14) 13 17
40: 52 type=186 (LJ14) 13 18
40: 53 type=193 (LJ14) 14 16
40: 54 type=193 (LJ14) 14 17
40: 55 type=186 (LJ14) 14 18
40: 56 type=190 (LJ14) 16 19
40: 57 type=190 (LJ14) 16 20
40: 58 type=190 (LJ14) 16 21
40: 59 type=190 (LJ14) 17 19
40: 60 type=190 (LJ14) 17 20
40: 61 type=190 (LJ14) 17 21
40: 62 type=196 (LJ14) 22 27
40: 63 type=197 (LJ14) 22 28
40: 64 type=198 (LJ14) 22 38
40: 65 type=190 (LJ14) 23 25
40: 66 type=195 (LJ14) 23 26
40: 67 type=186 (LJ14) 24 29
40: 68 type=187 (LJ14) 24 30
40: 69 type=187 (LJ14) 24 34
40: 70 type=188 (LJ14) 24 39
40: 71 type=189 (LJ14) 24 40
40: 72 type=190 (LJ14) 25 27
40: 73 type=190 (LJ14) 25 28
40: 74 type=190 (LJ14) 25 38
40: 75 type=191 (LJ14) 26 31
40: 76 type=191 (LJ14) 26 32
40: 77 type=191 (LJ14) 26 33
40: 78 type=191 (LJ14) 26 35
40: 79 type=191 (LJ14) 26 36
40: 80 type=191 (LJ14) 26 37
40: 81 type=190 (LJ14) 26 41
40: 82 type=192 (LJ14) 26 42
40: 83 type=193 (LJ14) 27 29
40: 84 type=191 (LJ14) 27 30
40: 85 type=191 (LJ14) 27 34
40: 86 type=194 (LJ14) 27 39
40: 87 type=186 (LJ14) 27 40
40: 88 type=195 (LJ14) 28 39
40: 89 type=187 (LJ14) 28 40
40: 90 type=193 (LJ14) 29 31
40: 91 type=193 (LJ14) 29 32
40: 92 type=193 (LJ14) 29 33
40: 93 type=193 (LJ14) 29 35
40: 94 type=193 (LJ14) 29 36
40: 95 type=193 (LJ14) 29 37
40: 96 type=196 (LJ14) 29 38
40: 97 type=191 (LJ14) 30 35
40: 98 type=191 (LJ14) 30 36
40: 99 type=191 (LJ14) 30 37
40: 100 type=197 (LJ14) 30 38
40: 101 type=191 (LJ14) 31 34
40: 102 type=191 (LJ14) 32 34
40: 103 type=191 (LJ14) 33 34
40: 104 type=197 (LJ14) 34 38
40: 105 type=196 (LJ14) 38 43
40: 106 type=197 (LJ14) 38 44
40: 107 type=198 (LJ14) 38 58
40: 108 type=190 (LJ14) 39 41
40: 109 type=195 (LJ14) 39 42
40: 110 type=186 (LJ14) 40 45
40: 111 type=186 (LJ14) 40 46
40: 112 type=199 (LJ14) 40 47
40: 113 type=188 (LJ14) 40 59
40: 114 type=189 (LJ14) 40 60
40: 115 type=190 (LJ14) 41 43
40: 116 type=190 (LJ14) 41 44
40: 117 type=190 (LJ14) 41 58
40: 118 type=200 (LJ14) 42 48
40: 119 type=200 (LJ14) 42 50
40: 120 type=190 (LJ14) 42 61
40: 121 type=192 (LJ14) 42 62
40: 122 type=193 (LJ14) 43 45
40: 123 type=193 (LJ14) 43 46
40: 124 type=201 (LJ14) 43 47
40: 125 type=194 (LJ14) 43 59
40: 126 type=186 (LJ14) 43 60
40: 127 type=202 (LJ14) 44 49
40: 128 type=202 (LJ14) 44 51
40: 129 type=200 (LJ14) 44 52
40: 130 type=200 (LJ14) 44 54
40: 131 type=195 (LJ14) 44 59
40: 132 type=187 (LJ14) 44 60
40: 133 type=201 (LJ14) 45 48
40: 134 type=201 (LJ14) 45 50
40: 135 type=196 (LJ14) 45 58
40: 136 type=201 (LJ14) 46 48
40: 137 type=201 (LJ14) 46 50
40: 138 type=196 (LJ14) 46 58
40: 139 type=203 (LJ14) 47 53
40: 140 type=203 (LJ14) 47 55
40: 141 type=204 (LJ14) 47 56
40: 142 type=205 (LJ14) 47 58
40: 143 type=203 (LJ14) 48 51
40: 144 type=204 (LJ14) 48 54
40: 145 type=203 (LJ14) 48 57
40: 146 type=203 (LJ14) 49 50
40: 147 type=206 (LJ14) 49 53
40: 148 type=203 (LJ14) 49 56
40: 149 type=204 (LJ14) 50 52
40: 150 type=203 (LJ14) 50 57
40: 151 type=206 (LJ14) 51 55
40: 152 type=203 (LJ14) 51 56
40: 153 type=203 (LJ14) 52 55
40: 154 type=203 (LJ14) 53 54
40: 155 type=206 (LJ14) 53 57
40: 156 type=206 (LJ14) 55 57
40: 157 type=196 (LJ14) 58 63
40: 158 type=196 (LJ14) 58 64
40: 159 type=198 (LJ14) 58 65
40: 160 type=190 (LJ14) 59 61
40: 161 type=195 (LJ14) 59 62
40: 162 type=188 (LJ14) 60 66
40: 163 type=189 (LJ14) 60 67
40: 164 type=190 (LJ14) 61 63
40: 165 type=190 (LJ14) 61 64
40: 166 type=190 (LJ14) 61 65
40: 167 type=190 (LJ14) 62 68
40: 168 type=192 (LJ14) 62 69
40: 169 type=194 (LJ14) 63 66
40: 170 type=186 (LJ14) 63 67
40: 171 type=194 (LJ14) 64 66
40: 172 type=186 (LJ14) 64 67
40: 173 type=196 (LJ14) 65 70
40: 174 type=197 (LJ14) 65 71
40: 175 type=198 (LJ14) 65 89
40: 176 type=190 (LJ14) 66 68
40: 177 type=195 (LJ14) 66 69
40: 178 type=186 (LJ14) 67 72
40: 179 type=186 (LJ14) 67 73
40: 180 type=187 (LJ14) 67 74
40: 181 type=188 (LJ14) 67 90
40: 182 type=189 (LJ14) 67 91
40: 183 type=190 (LJ14) 68 70
40: 184 type=190 (LJ14) 68 71
40: 185 type=190 (LJ14) 68 89
40: 186 type=191 (LJ14) 69 75
40: 187 type=191 (LJ14) 69 76
40: 188 type=192 (LJ14) 69 77
40: 189 type=190 (LJ14) 69 92
40: 190 type=192 (LJ14) 69 93
40: 191 type=193 (LJ14) 70 72
40: 192 type=193 (LJ14) 70 73
40: 193 type=191 (LJ14) 70 74
40: 194 type=194 (LJ14) 70 90
40: 195 type=186 (LJ14) 70 91
40: 196 type=191 (LJ14) 71 78
40: 197 type=191 (LJ14) 71 79
40: 198 type=187 (LJ14) 71 80
40: 199 type=195 (LJ14) 71 90
40: 200 type=187 (LJ14) 71 91
40: 201 type=193 (LJ14) 72 75
40: 202 type=193 (LJ14) 72 76
40: 203 type=191 (LJ14) 72 77
40: 204 type=196 (LJ14) 72 89
40: 205 type=193 (LJ14) 73 75
40: 206 type=193 (LJ14) 73 76
40: 207 type=191 (LJ14) 73 77
40: 208 type=196 (LJ14) 73 89
40: 209 type=190 (LJ14) 74 81
40: 210 type=207 (LJ14) 74 82
40: 211 type=197 (LJ14) 74 89
40: 212 type=193 (LJ14) 75 78
40: 213 type=193 (LJ14) 75 79
40: 214 type=186 (LJ14) 75 80
40: 215 type=193 (LJ14) 76 78
40: 216 type=193 (LJ14) 76 79
40: 217 type=186 (LJ14) 76 80
40: 218 type=187 (LJ14) 77 83
40: 219 type=187 (LJ14) 77 86
40: 220 type=190 (LJ14) 78 81
40: 221 type=208 (LJ14) 78 82
40: 222 type=190 (LJ14) 79 81
40: 223 type=208 (LJ14) 79 82
40: 224 type=190 (LJ14) 80 84
40: 225 type=190 (LJ14) 80 85
40: 226 type=190 (LJ14) 80 87
40: 227 type=190 (LJ14) 80 88
40: 228 type=190 (LJ14) 81 83
40: 229 type=190 (LJ14) 81 86
40: 230 type=190 (LJ14) 83 87
40: 231 type=190 (LJ14) 83 88
40: 232 type=190 (LJ14) 84 86
40: 233 type=190 (LJ14) 85 86
40: 234 type=196 (LJ14) 89 94
40: 235 type=197 (LJ14) 89 95
40: 236 type=198 (LJ14) 89 100
40: 237 type=190 (LJ14) 90 92
40: 238 type=195 (LJ14) 90 93
40: 239 type=186 (LJ14) 91 96
40: 240 type=186 (LJ14) 91 97
40: 241 type=209 (LJ14) 91 98
40: 242 type=188 (LJ14) 91 101
40: 243 type=189 (LJ14) 91 102
40: 244 type=190 (LJ14) 92 94
40: 245 type=190 (LJ14) 92 95
40: 246 type=190 (LJ14) 92 100
40: 247 type=190 (LJ14) 93 99
40: 248 type=190 (LJ14) 93 103
40: 249 type=192 (LJ14) 93 104
40: 250 type=193 (LJ14) 94 96
40: 251 type=193 (LJ14) 94 97
40: 252 type=210 (LJ14) 94 98
40: 253 type=194 (LJ14) 94 101
40: 254 type=186 (LJ14) 94 102
40: 255 type=195 (LJ14) 95 101
40: 256 type=187 (LJ14) 95 102
40: 257 type=190 (LJ14) 96 99
40: 258 type=196 (LJ14) 96 100
40: 259 type=190 (LJ14) 97 99
40: 260 type=196 (LJ14) 97 100
40: 261 type=211 (LJ14) 98 100
40: 262 type=196 (LJ14) 100 105
40: 263 type=197 (LJ14) 100 106
40: 264 type=198 (LJ14) 100 115
40: 265 type=190 (LJ14) 101 103
40: 266 type=195 (LJ14) 101 104
40: 267 type=186 (LJ14) 102 107
40: 268 type=186 (LJ14) 102 108
40: 269 type=187 (LJ14) 102 109
40: 270 type=188 (LJ14) 102 116
40: 271 type=189 (LJ14) 102 117
40: 272 type=190 (LJ14) 103 105
40: 273 type=190 (LJ14) 103 106
40: 274 type=190 (LJ14) 103 115
40: 275 type=191 (LJ14) 104 110
40: 276 type=191 (LJ14) 104 111
40: 277 type=197 (LJ14) 104 112
40: 278 type=190 (LJ14) 104 118
40: 279 type=192 (LJ14) 104 119
40: 280 type=193 (LJ14) 105 107
40: 281 type=193 (LJ14) 105 108
40: 282 type=191 (LJ14) 105 109
40: 283 type=194 (LJ14) 105 116
40: 284 type=186 (LJ14) 105 117
40: 285 type=195 (LJ14) 106 113
40: 286 type=195 (LJ14) 106 114
40: 287 type=195 (LJ14) 106 116
40: 288 type=187 (LJ14) 106 117
40: 289 type=193 (LJ14) 107 110
40: 290 type=193 (LJ14) 107 111
40: 291 type=196 (LJ14) 107 112
40: 292 type=196 (LJ14) 107 115
40: 293 type=193 (LJ14) 108 110
40: 294 type=193 (LJ14) 108 111
40: 295 type=196 (LJ14) 108 112
40: 296 type=196 (LJ14) 108 115
40: 297 type=197 (LJ14) 109 115
40: 298 type=194 (LJ14) 110 113
40: 299 type=194 (LJ14) 110 114
40: 300 type=194 (LJ14) 111 113
40: 301 type=194 (LJ14) 111 114
40: 302 type=196 (LJ14) 115 120
40: 303 type=197 (LJ14) 115 121
40: 304 type=198 (LJ14) 115 134
40: 305 type=190 (LJ14) 116 118
40: 306 type=195 (LJ14) 116 119
40: 307 type=186 (LJ14) 117 122
40: 308 type=186 (LJ14) 117 123
40: 309 type=187 (LJ14) 117 124
40: 310 type=188 (LJ14) 117 135
40: 311 type=189 (LJ14) 117 136
40: 312 type=190 (LJ14) 118 120
40: 313 type=190 (LJ14) 118 121
40: 314 type=190 (LJ14) 118 134
40: 315 type=191 (LJ14) 119 125
40: 316 type=192 (LJ14) 119 126
40: 317 type=192 (LJ14) 119 130
40: 318 type=190 (LJ14) 119 137
40: 319 type=192 (LJ14) 119 138
40: 320 type=193 (LJ14) 120 122
40: 321 type=193 (LJ14) 120 123
40: 322 type=191 (LJ14) 120 124
40: 323 type=194 (LJ14) 120 135
40: 324 type=186 (LJ14) 120 136
40: 325 type=191 (LJ14) 121 127
40: 326 type=191 (LJ14) 121 128
40: 327 type=191 (LJ14) 121 129
40: 328 type=191 (LJ14) 121 131
40: 329 type=191 (LJ14) 121 132
40: 330 type=191 (LJ14) 121 133
40: 331 type=195 (LJ14) 121 135
40: 332 type=187 (LJ14) 121 136
40: 333 type=193 (LJ14) 122 125
40: 334 type=191 (LJ14) 122 126
40: 335 type=191 (LJ14) 122 130
40: 336 type=196 (LJ14) 122 134
40: 337 type=193 (LJ14) 123 125
40: 338 type=191 (LJ14) 123 126
40: 339 type=191 (LJ14) 123 130
40: 340 type=196 (LJ14) 123 134
40: 341 type=197 (LJ14) 124 134
40: 342 type=193 (LJ14) 125 127
40: 343 type=193 (LJ14) 125 128
40: 344 type=193 (LJ14) 125 129
40: 345 type=193 (LJ14) 125 131
40: 346 type=193 (LJ14) 125 132
40: 347 type=193 (LJ14) 125 133
40: 348 type=191 (LJ14) 126 131
40: 349 type=191 (LJ14) 126 132
40: 350 type=191 (LJ14) 126 133
40: 351 type=191 (LJ14) 127 130
40: 352 type=191 (LJ14) 128 130
40: 353 type=191 (LJ14) 129 130
40: 354 type=196 (LJ14) 134 139
40: 355 type=197 (LJ14) 134 140
40: 356 type=198 (LJ14) 134 144
40: 357 type=190 (LJ14) 135 137
40: 358 type=195 (LJ14) 135 138
40: 359 type=186 (LJ14) 136 141
40: 360 type=186 (LJ14) 136 142
40: 361 type=186 (LJ14) 136 143
40: 362 type=188 (LJ14) 136 145
40: 363 type=189 (LJ14) 136 146
40: 364 type=190 (LJ14) 137 139
40: 365 type=190 (LJ14) 137 140
40: 366 type=190 (LJ14) 137 144
40: 367 type=190 (LJ14) 138 147
40: 368 type=192 (LJ14) 138 148
40: 369 type=193 (LJ14) 139 141
40: 370 type=193 (LJ14) 139 142
40: 371 type=193 (LJ14) 139 143
40: 372 type=194 (LJ14) 139 145
40: 373 type=186 (LJ14) 139 146
40: 374 type=195 (LJ14) 140 145
40: 375 type=187 (LJ14) 140 146
40: 376 type=196 (LJ14) 141 144
40: 377 type=196 (LJ14) 142 144
40: 378 type=196 (LJ14) 143 144
40: 379 type=196 (LJ14) 144 149
40: 380 type=197 (LJ14) 144 150
40: 381 type=198 (LJ14) 144 154
40: 382 type=190 (LJ14) 145 147
40: 383 type=195 (LJ14) 145 148
40: 384 type=186 (LJ14) 146 151
40: 385 type=186 (LJ14) 146 152
40: 386 type=186 (LJ14) 146 153
40: 387 type=188 (LJ14) 146 155
40: 388 type=190 (LJ14) 147 149
40: 389 type=190 (LJ14) 147 150
40: 390 type=190 (LJ14) 147 154
40: 391 type=193 (LJ14) 149 151
40: 392 type=193 (LJ14) 149 152
40: 393 type=193 (LJ14) 149 153
40: 394 type=194 (LJ14) 149 155
40: 395 type=195 (LJ14) 150 155
40: 396 type=196 (LJ14) 151 154
40: 397 type=196 (LJ14) 152 154
40: 398 type=196 (LJ14) 153 154
40: Coulomb-14:
40: nr: 0
40: LJC-14 q:
40: nr: 0
40: LJC Pairs NB:
40: nr: 0
40: LJ (SR):
40: nr: 0
40: Buck.ham (SR):
40: nr: 0
40: LJ (unused):
40: nr: 0
40: B.ham (unused):
40: nr: 0
40: Disper. corr.:
40: nr: 0
40: Coulomb (SR):
40: nr: 0
40: Coul (unused):
40: nr: 0
40: RF excl.:
40: nr: 0
40: Coul. recip.:
40: nr: 0
40: LJ recip.:
40: nr: 0
40: DPD:
40: nr: 0
40: Polarization:
40: nr: 0
40: Water Pol.:
40: nr: 0
40: Thole Pol.:
40: nr: 0
40: Anharm. Pol.:
40: nr: 0
40: Position Rest.:
40: nr: 0
40: Flat-bottom posres:
40: nr: 0
40: Dis. Rest.:
40: nr: 0
40: D.R.Viol. (nm):
40: nr: 0
40: Orient. Rest.:
40: nr: 0
40: Ori. R. RMSD:
40: nr: 0
40: Angle Rest.:
40: nr: 0
40: Angle Rest. Z:
40: nr: 0
40: Dih. Rest.:
40: nr: 0
40: Dih. Rest. Viol.:
40: nr: 0
40: Constraint:
40: nr: 0
40: Constr. No Conn.:
40: nr: 0
40: Settle:
40: nr: 0
40: Virtual site 2:
40: nr: 0
40: Virtual site 2fd:
40: nr: 0
40: Virtual site 3:
40: nr: 0
40: Virtual site 3fd:
40: nr: 0
40: Virtual site 3fad:
40: nr: 0
40: Virtual site 3out:
40: nr: 0
40: Virtual site 4fd:
40: nr: 0
40: Virtual site 4fdn:
40: nr: 0
40: Virtual site N:
40: nr: 0
40: COM Pull En.:
40: nr: 0
40: Density fitting:
40: nr: 0
40: Quantum En.:
40: nr: 0
40: Potential:
40: nr: 0
40: Kinetic En.:
40: nr: 0
40: Total Energy:
40: nr: 0
40: Conserved En.:
40: nr: 0
40: Temperature:
40: nr: 0
40: Vir. Temp. (not used):
40: nr: 0
40: Pres. DC:
40: nr: 0
40: Pressure:
40: nr: 0
40: dH/dl constr.:
40: nr: 0
40: dVremain/dl:
40: nr: 0
40: dEkin/dl:
40: nr: 0
40: dVcoul/dl:
40: nr: 0
40: dVvdw/dl:
40: nr: 0
40: dVbonded/dl:
40: nr: 0
40: dVrestraint/dl:
40: nr: 0
40: dVtemperature/dl:
40: nr: 0
40: grp[T-Coupling ] nr=1, name=[ rest]
40: grp[Energy Mon. ] nr=1, name=[ rest]
40: grp[Acceleration] nr=1, name=[ rest]
40: grp[Freeze ] nr=1, name=[ rest]
40: grp[User1 ] nr=1, name=[ rest]
40: grp[User2 ] nr=1, name=[ rest]
40: grp[VCM ] nr=1, name=[ rest]
40: grp[Compressed X] nr=1, name=[ rest]
40: grp[Or. Res. Fit] nr=1, name=[ rest]
40: grp[QMMM ] nr=1, name=[ rest]
40: grpname (11):
40: grpname[0]={name="System"}
40: grpname[1]={name="Protein"}
40: grpname[2]={name="Protein-H"}
40: grpname[3]={name="C-alpha"}
40: grpname[4]={name="Backbone"}
40: grpname[5]={name="MainChain"}
40: grpname[6]={name="MainChain+Cb"}
40: grpname[7]={name="MainChain+H"}
40: grpname[8]={name="SideChain"}
40: grpname[9]={name="SideChain-H"}
40: grpname[10]={name="rest"}
40: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
40: allocated 0 0 0 0 0 0 0 0 0 0
40: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
40: box (3x3):
40: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
40: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
40: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
40: box_rel (3x3):
40: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv (3x3):
40: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev (3x3):
40: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev (3x3):
40: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev (3x3):
40: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: nosehoover_xi: not available
40: x (156x3):
40: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
40: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
40: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
40: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
40: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
40: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
40: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
40: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
40: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
40: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
40: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
40: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
40: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
40: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
40: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
40: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
40: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
40: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
40: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
40: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
40: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
40: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
40: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
40: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
40: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
40: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
40: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
40: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
40: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
40: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
40: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
40: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
40: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
40: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
40: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
40: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
40: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
40: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
40: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
40: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
40: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
40: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
40: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
40: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
40: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
40: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
40: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
40: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
40: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
40: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
40: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
40: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
40: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
40: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
40: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
40: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
40: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
40: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
40: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
40: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
40: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
40: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
40: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
40: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
40: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
40: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
40: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
40: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
40: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
40: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
40: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
40: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
40: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
40: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
40: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
40: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
40: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
40: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
40: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
40: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
40: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
40: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
40: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
40: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
40: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
40: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
40: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
40: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
40: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
40: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
40: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
40: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
40: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
40: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
40: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
40: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
40: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
40: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
40: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
40: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
40: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
40: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
40: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
40: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
40: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
40: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
40: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
40: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
40: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
40: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
40: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
40: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
40: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
40: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
40: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
40: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
40: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
40: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
40: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
40: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
40: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
40: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
40: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
40: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
40: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
40: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
40: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
40: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
40: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
40: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
40: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
40: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
40: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
40: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
40: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
40: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
40: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
40: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
40: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
40: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
40: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
40: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
40: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
40: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
40: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
40: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
40: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
40: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
40: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
40: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
40: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
40: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
40: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
40: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
40: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
40: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
40: v (156x3):
40: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: Group statistics
40: T-Coupling : 156 (total 156 atoms)
40: Energy Mon. : 156 (total 156 atoms)
40: Acceleration: 156 (total 156 atoms)
40: Freeze : 156 (total 156 atoms)
40: User1 : 156 (total 156 atoms)
40: User2 : 156 (total 156 atoms)
40: VCM : 156 (total 156 atoms)
40: Compressed X: 156 (total 156 atoms)
40: Or. Res. Fit: 156 (total 156 atoms)
40: QMMM : 156 (total 156 atoms)
40: [ OK ] DumpTest.WorksWithTpr (60 ms)
40: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
40: [ OK ] DumpTest.WorksWithTprAndMdpWriting (8 ms)
40: [----------] 2 tests from DumpTest (68 ms total)
40:
40: [----------] 4 tests from ReportMethodsTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -978130193
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (1 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectInformation
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
40: [ OK ] ReportMethodsTest.WritesCorrectInformation (5 ms)
40: [ RUN ] ReportMethodsTest.ToolEndToEndTest
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
40: section: Methods
40: subsection: Simulation system
40: A system of 1 molecules (156 atoms) was simulated.
40:
40: subsection: Simulation settings
40: A total of 0 ns were simulated with a time step of 1 fs.
40: Neighbor searching was performed every 10 steps.
40: The Cut-off algorithm was used for electrostatic interactions.
40: with a cut-off of 1 nm.
40: A single cut-off of 1.1 nm was used for Van der Waals interactions.
40: [ OK ] ReportMethodsTest.ToolEndToEndTest (6 ms)
40: [----------] 4 tests from ReportMethodsTest (12 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (17 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (16 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (15 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (14 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (93 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (25 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 18 tests from 4 test cases ran. (9175 ms total)
40: [ PASSED ] 18 tests.
40/52 Test #40: ToolUnitTests ....................... Passed 9.25 sec
test 41
Start 41: FileIOTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 33 tests from 8 test cases.
41: [----------] Global test environment set-up.
41: [----------] 2 tests from FileMD5Test
41: [ RUN ] FileMD5Test.CanComputeMD5
41: [ OK ] FileMD5Test.CanComputeMD5 (4 ms)
41: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
41: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
41: [----------] 2 tests from FileMD5Test (6 ms total)
41:
41: [----------] 3 tests from MrcSerializer
41: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
41: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
41: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (1 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
41: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (4 ms)
41: [----------] 3 tests from MrcSerializer (5 ms total)
41:
41: [----------] 4 tests from MrcDensityMap
41: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
41: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms)
41: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
41: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
41: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
41: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
41: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
41: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (18 ms)
41: [----------] 4 tests from MrcDensityMap (26 ms total)
41:
41: [----------] 8 tests from MrcDensityMapHeaderTest
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
41: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (1 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.IsSane
41: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
41: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
41:
41: [----------] 9 tests from ReadTest
41: [ RUN ] ReadTest.get_eint_ReadsInteger
41: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
41: [ RUN ] ReadTest.get_eint64_ReadsInteger
41: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsInteger
41: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsFloat
41: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
41: [ RUN ] ReadTest.get_ereal_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not a
41: real value
41:
41:
41: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
41: [----------] 9 tests from ReadTest (1 ms total)
41:
41: [----------] 1 test from FileIOXdrSerializerTest
41: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
41: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
41: [----------] 1 test from FileIOXdrSerializerTest (1 ms total)
41:
41: [----------] 2 tests from TngTest
41: [ RUN ] TngTest.CanOpenTngFile
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: [ OK ] TngTest.CanOpenTngFile (1 ms)
41: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
41: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
41: [----------] 2 tests from TngTest (1 ms total)
41:
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (9 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms)
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (18 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 33 tests from 8 test cases ran. (59 ms total)
41: [ PASSED ] 33 tests.
41/52 Test #41: FileIOTests ......................... Passed 0.13 sec
test 42
Start 42: SelectionUnitTests
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
42: Test timeout computed to be: 30
42: [==========] Running 192 tests from 11 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from IndexGroupTest
42: [ RUN ] IndexGroupTest.RemovesDuplicates
42: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
42: [----------] 1 test from IndexGroupTest (1 ms total)
42:
42: [----------] 15 tests from IndexBlockTest
42: [ RUN ] IndexBlockTest.CreatesUnknownBlock
42: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms)
42: [ RUN ] IndexBlockTest.CreatesAtomBlock
42: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (2 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesSingleBlock
42: [ OK ] IndexBlockTest.CreatesSingleBlock (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
42: [----------] 15 tests from IndexBlockTest (8 ms total)
42:
42: [----------] 11 tests from IndexMapTest
42: [ RUN ] IndexMapTest.InitializesAtomBlock
42: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
42: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
42: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
42: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms)
42: [ RUN ] IndexMapTest.InitializesMoleculeBlock
42: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
42: [ RUN ] IndexMapTest.MapsSingleBlock
42: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocks
42: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
42: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms)
42: [ RUN ] IndexMapTest.HandlesMultipleRequests
42: [ OK ] IndexMapTest.HandlesMultipleRequests (2 ms)
42: [----------] 11 tests from IndexMapTest (13 ms total)
42:
42: [----------] 3 tests from IndexGroupsAndNamesTest
42: [ RUN ] IndexGroupsAndNamesTest.containsNames
42: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
42: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
42: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms)
42: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
42: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
42: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
42:
42: [----------] 15 tests from NeighborhoodSearchTest
42: [ RUN ] NeighborhoodSearchTest.SimpleSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSearch (76 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
42: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (79 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchBox
42: [ OK ] NeighborhoodSearchTest.GridSearchBox (13 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
42: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (49 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
42: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (25 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
42: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (13 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
42: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (14 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (214 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
42: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
42: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (1 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
42: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (17 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
42: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (5 ms)
42: [----------] 15 tests from NeighborhoodSearchTest (509 ms total)
42:
42: [----------] 12 tests from PositionCalculationTest
42: [ RUN ] PositionCalculationTest.ComputesAtomPositions
42: [ OK ] PositionCalculationTest.ComputesAtomPositions (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionMask
42: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
42: [----------] 12 tests from PositionCalculationTest (17 ms total)
42:
42: [----------] 29 tests from SelectionCollectionTest
42: [ RUN ] SelectionCollectionTest.HandlesNoSelections
42: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
42: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
42: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
42: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
42: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
42: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
42: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
42: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
42: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
42: [----------] 29 tests from SelectionCollectionTest (52 ms total)
42:
42: [----------] 14 tests from SelectionCollectionInteractiveTest
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
42: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
42: [----------] 14 tests from SelectionCollectionInteractiveTest (35 ms total)
42:
42: [----------] 66 tests from SelectionCollectionDataTest
42: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
42: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
42: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResnr
42: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
42: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
42: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
42: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesChain
42: [ OK ] SelectionCollectionDataTest.HandlesChain (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMass
42: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCharge
42: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
42: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
42: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
42: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBeta
42: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResname
42: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (17 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (26 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
42: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (12 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (9 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
42: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
42: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
42: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
42: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
42: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
42: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
42: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
42: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
42: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
42: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
42: [----------] 66 tests from SelectionCollectionDataTest (328 ms total)
42:
42: [----------] 17 tests from SelectionOptionTest
42: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
42: [ OK ] SelectionOptionTest.ParsesSimpleSelection (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
42: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
42: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
42: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptySelections
42: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
42: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelections
42: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
42: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesAdjuster
42: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
42: [----------] 17 tests from SelectionOptionTest (23 ms total)
42:
42: [----------] 9 tests from SelectionFileOptionTest
42: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
42: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (2 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
42: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
42: [----------] 9 tests from SelectionFileOptionTest (13 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 192 tests from 11 test cases ran. (1002 ms total)
42: [ PASSED ] 192 tests.
42/52 Test #42: SelectionUnitTests .................. Passed 1.09 sec
test 43
Start 43: MdrunTests
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 96 tests from 23 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -231246593
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.85654101644806e+03
43: Maximum force = 2.88468568366558e+03 on atom 3
43: Norm of force = 1.07544474716821e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (81 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to 1070430200
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.71386626596691e+04
43: Maximum force = 4.34097106676756e+03 on atom 2
43: Norm of force = 1.25497916295893e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (38 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (38 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to -1067837026
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.638 0.319 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.812 29.572
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.423 0.211 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.043 11.749
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (578 ms)
43: [----------] 4 tests from DensityFittingTest (735 ms total)
43:
43: [----------] 3 tests from GromppTest
43: [ RUN ] GromppTest.EmptyMdpFileWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -413630315
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.EmptyMdpFileWorks (23 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 112595329
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group rest: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorks (24 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -100382405
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group Methanol: Single, 3 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 3.0 280.0
43: 6.0- 270.0
43: Simulated annealing for group SOL: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group Methanol is 7.20
43: Number of degrees of freedom in T-Coupling group SOL is 4.80
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (24 ms)
43: [----------] 3 tests from GromppTest (71 ms total)
43:
43: [----------] 1 test from MdrunTest
43: [ RUN ] MdrunTest.WritesHelp
43: [ OK ] MdrunTest.WritesHelp (31 ms)
43: [----------] 1 test from MdrunTest (31 ms total)
43:
43: [----------] 1 test from OriresTest
43: [ RUN ] OriresTest.OriresCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to -782502570
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 518.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
43: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
43:
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
43: 10 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.631 0.316 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.021 3.986
43: [ OK ] OriresTest.OriresCanRun (2247 ms)
43: [----------] 1 test from OriresTest (2247 ms total)
43:
43: [----------] 3 tests from PmeTest
43: [ RUN ] PmeTest.ReproducesEnergies
43: Setting the LD random seed to 893723299
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.818 0.409 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.435 5.411
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.197 0.599 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.031 7.918
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.793 0.397 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.572 5.250
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (1658 ms)
43: [ RUN ] PmeTest.ScalesTheBox
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -998713757
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.019 0.010 193.5
43: (ns/day) (hour/ns)
43: Performance: 8.720 2.752
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBox (76 ms)
43: [ RUN ] PmeTest.ScalesTheBoxWithWalls
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 289579426
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Searching the wall atom type(s)
43: Number of degrees of freedom in T-Coupling group rest is 13.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: NVE simulation: will use the initial temperature of 966.268 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.097 0.049 198.4
43: (ns/day) (hour/ns)
43: Performance: 1.772 13.542
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBoxWithWalls (211 ms)
43: [----------] 3 tests from PmeTest (1947 ms total)
43:
43: [----------] 1 test from CompelTest
43: [ RUN ] CompelTest.SwapCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to 1316727629
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 1 bonded neighbours molecule type 'NA'
43: Excluding 1 bonded neighbours molecule type 'CL'
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Split0 group 'Ch0' contains 83 atoms.
43: Split1 group 'Ch1' contains 83 atoms.
43: Solvent group 'SOL' contains 11931 atoms.
43: Swap group 'NA+' contains 19 atoms.
43: Swap group 'CL-' contains 19 atoms.
43: Number of degrees of freedom in T-Coupling group System is 27869.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: Removing center of mass motion in the presence of position restraints
43: might cause artifacts. When you are using position restraints to
43: equilibrate a macro-molecule, the artifacts are usually negligible.
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Determining initial numbers of ions per compartment.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 2 steps, 0.0 ps.
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 1 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 7.203 3.602 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.360 66.698
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Copying channel fluxes from checkpoint file data
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 6.474 3.238 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.400 59.954
43: [ OK ] CompelTest.SwapCanRun (12724 ms)
43: [----------] 1 test from CompelTest (12724 ms total)
43:
43: [----------] 6 tests from BondedInteractionsTest
43: [ RUN ] BondedInteractionsTest.NormalBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1352285678
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 186.5
43: (ns/day) (hour/ns)
43: Performance: 46.520 0.516
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalBondWorks (38 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -598760691
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 187.2
43: (ns/day) (hour/ns)
43: Performance: 44.033 0.545
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedBondWorks (80 ms)
43: [ RUN ] BondedInteractionsTest.NormalAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1036314768
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.6
43: (ns/day) (hour/ns)
43: Performance: 50.521 0.475
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalAngleWorks (38 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1046034467
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 186.7
43: (ns/day) (hour/ns)
43: Performance: 44.318 0.542
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (47 ms)
43: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 752271443
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.7
43: (ns/day) (hour/ns)
43: Performance: 49.936 0.481
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalDihedralWorks (38 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 39079505
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 187.1
43: (ns/day) (hour/ns)
43: Performance: 44.629 0.538
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (47 ms)
43: [----------] 6 tests from BondedInteractionsTest (288 ms total)
43:
43: [----------] 6 tests from MdrunTerminationTest
43: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
43: Setting the LD random seed to -2077884062
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.464 0.232 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.117 21.492
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.372 0.186 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.394 17.222
43: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (468 ms)
43: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
43: Setting the LD random seed to 514606863
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 1, rlist from 1.024 to 1
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 100 steps, 0.1 ps.
43:
43: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.393 0.197 199.7
43: (ns/day) (hour/ns)
43: Performance: 0.878 27.339
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 102
43: Writing statusfile with starting step 0 and length 102 steps...
43: time 0.000 and length 0.102 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.373 0.187 199.7
43: (ns/day) (hour/ns)
43: Performance: 47.216 0.508
43: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (434 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
43: Setting the LD random seed to -2055116135
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.394 0.197 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.315 18.253
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.462 0.231 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.122 21.389
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 6
43: Writing statusfile with starting step 0 and length 6 steps...
43: time 0.000 and length 0.006 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.497 0.249 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.042 23.034
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 8
43: Writing statusfile with starting step 0 and length 8 steps...
43: time 0.000 and length 0.008 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.545 0.272 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.952 25.222
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.001 0.001 167.7
43: (ns/day) (hour/ns)
43: Performance: 111.196 0.216
43: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (1052 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
43: Setting the LD random seed to 1540315205
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.573 0.287 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.903 26.566
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.588 0.294 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.468 16.349
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (637 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
43: Setting the LD random seed to 1523783728
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.520 0.260 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.996 24.086
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (304 ms)
43: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
43: Setting the LD random seed to -1907158343
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.533 0.267 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.972 24.701
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.522 0.261 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.993 24.177
43: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (585 ms)
43: [----------] 6 tests from MdrunTerminationTest (3481 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1990772137
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 188.2
43: (ns/day) (hour/ns)
43: Performance: 45.744 0.525
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (40 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 686623968
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 188.2
43: (ns/day) (hour/ns)
43: Performance: 45.947 0.522
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (40 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1553842769
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 188.3
43: (ns/day) (hour/ns)
43: Performance: 45.744 0.525
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (39 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 861266556
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.006 0.003 192.0
43: (ns/day) (hour/ns)
43: Performance: 26.973 0.890
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (131 ms)
43: [----------] 4 tests from MimicTest (251 ms total)
43:
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
43: Setting the LD random seed to -11079135
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.734 0.367 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.470 51.019
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (403 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
43: Setting the LD random seed to 548386284
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.572 0.286 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.604 39.724
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (321 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
43: Setting the LD random seed to 1492742349
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.529 0.265 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.653 36.741
43:
Reading frame 0 time 0.000
43: # Atoms 3
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (300 ms)
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (1026 ms total)
43:
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.527 0.264 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.572 4.307
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.513 0.257 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.025 7.934
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.557 0.279 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.787 8.611
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (882 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.601 0.301 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.884 4.914
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.509 0.254 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.055 7.855
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.731 0.366 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.126 11.288
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1012 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.442 0.221 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.642 3.613
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.530 0.265 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.933 8.184
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.641 0.321 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.423 9.906
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (899 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.487 0.244 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.030 3.980
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.552 0.276 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.816 8.524
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.796 0.398 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.951 12.299
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1011 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.547 0.274 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.364 4.474
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.529 0.265 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.933 8.183
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.974 0.487 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.596 15.038
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (1121 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.973 0.486 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.019 7.949
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.530 0.265 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.933 8.183
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.575 0.288 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.704 8.877
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1133 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.509 0.255 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.760 4.167
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.443 0.222 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.507 6.844
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.124 1.062 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.732 32.788
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (1631 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.997 0.499 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.944 8.153
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.572 0.286 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.715 8.841
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.906 0.453 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.716 13.983
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1337 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.736 0.368 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.989 6.016
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.789 0.395 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.969 12.187
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.066 0.533 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.458 16.457
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (1655 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.740 0.370 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.965 6.053
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.789 0.395 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.968 12.196
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.772 0.386 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.013 11.921
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1500 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.169 1.085 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.354 17.728
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.715 0.358 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.172 11.052
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.558 0.279 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.783 8.622
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (2244 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.831 0.916 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.603 14.967
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.046 0.523 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.486 16.152
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.918 0.459 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.692 14.182
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (2356 ms)
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (16783 ms total)
43:
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.742 0.372 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.952 6.073
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.059 1.030 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.755 31.802
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.569 0.785 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.991 24.228
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (2478 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.800 0.400 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.672 6.536
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.898 0.449 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.731 13.862
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 6.871 3.436 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.226 106.045
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (4602 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.607 0.804 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.827 13.139
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.962 0.482 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.614 14.871
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.764 0.382 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.034 11.799
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (2245 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.077 0.539 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.725 8.808
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.724 0.363 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.143 11.198
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.812 0.906 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.858 27.969
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (2276 ms)
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (11603 ms total)
43:
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.658 0.329 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.461 5.380
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.574 0.287 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.707 8.866
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.819 0.410 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.898 12.647
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1119 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.530 0.265 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.536 4.335
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.663 0.332 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.343 10.243
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.990 0.995 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.782 30.710
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1685 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.692 0.846 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.736 13.825
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.641 0.321 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.424 9.900
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.575 0.287 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.705 8.873
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1548 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.529 0.265 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.548 4.326
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.485 0.243 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.201 7.498
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.640 0.320 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.427 9.889
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (922 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.509 0.255 199.9
43: (ns/day) (hour/ns)
43: Performance: 5.770 4.160
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.708 0.354 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.194 10.937
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.691 0.346 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.250 10.666
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (1043 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.763 0.382 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.849 6.235
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.335 0.668 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.164 20.611
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 3.290 1.645 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.473 50.776
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (2778 ms)
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (9096 ms total)
43:
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.531 0.266 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.524 4.345
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.041 0.521 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.492 16.082
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.530 0.265 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.929 8.194
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1145 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.796 0.398 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.689 6.505
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.597 0.299 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.602 9.224
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.619 0.310 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.510 9.562
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1100 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.625 0.313 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.696 5.111
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.601 0.301 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.583 9.292
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.645 0.323 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.408 9.968
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1020 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.320 0.660 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.225 10.787
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.669 0.335 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.325 10.325
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.690 0.345 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.254 10.649
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1423 ms)
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (4688 ms total)
43:
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.361 1.181 200.0
43: (ns/day) (hour/ns)
43: Performance: 1.244 19.290
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.510 0.255 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.047 7.876
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.685 0.843 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.923 26.011
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (2368 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.195 0.598 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.457 9.766
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.527 0.264 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.949 8.137
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.570 0.285 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.728 8.798
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1246 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.670 0.335 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.379 5.481
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.640 0.320 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.428 9.886
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.529 0.265 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.938 8.168
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1021 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.085 0.543 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.706 8.868
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.796 0.398 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.952 12.294
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.751 0.376 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.068 11.604
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1411 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.595 0.298 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.930 4.868
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.479 0.240 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.238 7.411
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.552 0.276 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.815 8.527
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (928 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.576 0.288 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.095 4.710
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.533 0.267 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.916 8.231
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.562 0.281 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.767 8.673
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (954 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.651 0.326 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.505 5.327
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.513 0.257 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.030 7.921
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.588 1.294 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.601 39.948
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (2428 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.978 0.989 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.485 16.163
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 5.113 2.557 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.304 78.920
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.189 0.595 199.9
43: (ns/day) (hour/ns)
43: Performance: 1.308 18.352
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (4238 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.741 0.371 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.964 6.054
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.598 0.299 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.599 9.235
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.752 0.376 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.067 11.612
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1135 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (15736 ms total)
43:
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
43: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.809 0.405 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.627 6.617
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.858 0.430 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.810 13.257
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.095 1.048 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.742 32.347
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1984 ms)
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (1985 ms total)
43:
43: [----------] 3 tests from Checking/InitialConstraintsTest
43: [ RUN ] Checking/InitialConstraintsTest.Works/0
43: Setting the LD random seed to -1933270972
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 2.160 1.080 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.160 150.030
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (1128 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/1
43: Setting the LD random seed to -1452220210
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.490 0.245 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.705 34.048
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (293 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: Integrator method md-vv-avek is implemented primarily for validation
43: purposes; for molecular dynamics, you should probably be using md or md-vv
43:
43: Setting the LD random seed to -1835912103
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.102 0.551 199.9
43: (ns/day) (hour/ns)
43: Performance: 0.314 76.549
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (599 ms)
43: [----------] 3 tests from Checking/InitialConstraintsTest (2020 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to 1514163018
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 60501.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.672 0.336 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.541 15.578
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1453 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to -1946962884
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 43675.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.19770464690297e+03
43: Maximum force = 1.77948604657896e+04 on atom 9
43: Norm of force = 7.87328617833980e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (1116 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (2570 ms total)
43:
43: [----------] 2 tests from Argon12/OutputFiles
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.758 0.379 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.875 6.194
43: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (416 ms)
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.603 0.802 200.0
43: (ns/day) (hour/ns)
43: Performance: 1.832 13.098
43: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (846 ms)
43: [----------] 2 tests from Argon12/OutputFiles (1262 ms total)
43:
43: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.713 0.356 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.120 5.825
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.705 0.353 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.163 5.765
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision)
43:
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (779 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.177 0.589 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.495 9.620
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.569 0.285 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.158 4.653
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (944 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 398.997 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
43: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.418 0.709 200.0
43: (ns/day) (hour/ns)
43: Performance: 2.072 11.584
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.545 0.273 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.385 4.457
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (5168 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.220 0.610 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.408 9.967
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.285 0.643 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.285 10.505
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (5400 ms)
43: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (12292 ms total)
43:
43: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.891 0.446 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.293 7.287
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.050 0.525 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.797 8.581
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (1028 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.590 0.295 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.977 4.823
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.672 0.336 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.369 5.494
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (689 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.633 0.317 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.640 5.173
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.716 0.358 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.102 5.851
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (733 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.700 0.350 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.195 5.722
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.715 0.358 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.104 5.848
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (767 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 398.997 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
43: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.596 0.298 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.922 4.876
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.579 0.290 199.9
43: (ns/day) (hour/ns)
43: Performance: 5.072 4.732
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (4736 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 398.997 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
43: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.796 0.399 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.686 6.512
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.707 0.353 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.156 5.775
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (4912 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.752 0.376 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.905 6.146
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.706 0.353 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.162 5.766
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (4878 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.218 0.610 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.410 9.959
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.794 0.397 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.700 6.487
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (5167 ms)
43: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (22910 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/Trajectories
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
43: Setting the LD random seed to 2139966960
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.580 0.290 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.082 11.528
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (340 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
43: Setting the LD random seed to -1878202753
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.522 0.262 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.312 10.379
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (311 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
43: Setting the LD random seed to -403397604
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.412 0.207 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.929 8.195
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (256 ms)
43: [----------] 3 tests from MdrunCanWrite/Trajectories (908 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
43: Setting the LD random seed to -795406933
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.503 0.252 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.030 23.309
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (299 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
43: Setting the LD random seed to 1782920668
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.459 0.230 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.127 21.301
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (278 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
43: Setting the LD random seed to 1207220570
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.437 0.219 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.184 20.268
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (266 ms)
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories (844 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 96 tests from 23 test cases ran. (125504 ms total)
43: [ PASSED ] 96 tests.
43/52 Test #43: MdrunTests .......................... Passed 125.64 sec
test 44
Start 44: MdrunNonIntegratorTests
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 65 tests from 7 test cases.
44: [----------] Global test environment set-up.
44: [----------] 1 test from NonbondedBenchTest
44: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
44: System size: 3000 atoms
44: Cut-off radius: 1 nm
44: Number of threads: 1
44: Number of iterations: 1
44: Compute energies: no
44: Ewald excl. corr.: analytical
44:
44: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
44: total useful
44: Ewald all geom. no 0.000 0.0000 inf inf
44: [ OK ] NonbondedBenchTest.BasicEndToEndTest (667 ms)
44: [----------] 1 test from NonbondedBenchTest (667 ms total)
44:
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -4.79910463671071e+01
44: Maximum force = 1.86297359432220e+02 on atom 13
44: Norm of force = 8.77219865482161e+01
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (4103 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 3.02331e+02 on atom 3
44: F-Norm = 1.18024e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -5.58622538633290e+01
44: Maximum force = 4.27274822366523e+02 on atom 13
44: Norm of force = 1.84530029253828e+02
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (4128 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.19376899751521e+02
44: Maximum force = 9.99884921009767e+03 on atom 9
44: Norm of force = 4.61669565054298e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1052 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44:
44: NOTE 3 [file glycine_vacuo.top, line 12]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41575e+04 on atom 10
44: F-Norm = 1.18451e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.51743018140925e+02
44: Maximum force = 7.42089573409111e+03 on atom 9
44: Norm of force = 3.56929298615739e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1048 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.56984193848276e+02
44: Maximum force = 4.56923624626296e+02 on atom 17
44: Norm of force = 1.83258377168331e+02
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (126 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44:
44: NOTE 4 [file unknown]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 1.06800e+03 on atom 28
44: F-Norm = 4.26922e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.69410778678185e+02
44: Maximum force = 2.18225948473957e+02 on atom 17
44: Norm of force = 7.92068036537697e+01
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (128 ms)
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (10586 ms total)
44:
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents converged to Fmax < 10 in 1 steps
44: Potential Energy = -9.74257075835450e-01
44: Maximum force = 4.01322929015108e+00 on atom 1
44: Norm of force = 1.63839399694368e+00
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (36 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.90642313893957e-01
44: Maximum force = 2.57812909491105e+00 on atom 1
44: Norm of force = 1.05251679559258e+00
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (36 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.90642313893957e-01
44: Maximum force = 2.57812909491105e+00 on atom 1
44: Norm of force = 1.05251679559258e+00
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (37 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.19395484891517e+02
44: Maximum force = 9.97041707197910e+03 on atom 9
44: Norm of force = 4.62274878665467e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1058 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.56258793899479e+02
44: Maximum force = 7.50181017480397e+03 on atom 9
44: Norm of force = 3.61390332564874e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1061 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 5.61116097794203e+02
44: Maximum force = 1.26854826291223e+04 on atom 10
44: Norm of force = 6.06436286976271e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1076 ms)
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3304 ms total)
44:
44: [----------] 5 tests from NormalModesWorks/NormalModesTest
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 15.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=6), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation '2 scaled waters'
44: 12 steps.
44:
44: Maximum force: 9.96989e-06
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.1-Raspbian-2020.1-1
44:
44: Diagonalizing to find vectors 7 through 18...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--18 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 6 Atoms
44: Using begin = 7 and end = 18
44: Full matrix storage format, nrow=18, ncols=18
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (69 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
44:
44: NOTE 3 [file villin.top, line 2452]:
44: System has non-zero total charge: -2.000000
44: Total charge should normally be an integer. See
44: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
44: for discussion on how close it should be to an integer.
44:
44:
44:
44: Number of degrees of freedom in T-Coupling group System is 765.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=256), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
44: 512 steps.
44:
44: Maximum force: 6.97568e-04
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.1-Raspbian-2020.1-1
44:
44: Diagonalizing to find vectors 7 through 50...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--50 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 256 Atoms
44: Using begin = 7 and end = 50
44: Full matrix storage format, nrow=768, ncols=768
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (20564 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 15.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=6), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation 'flex spc dimer'
44: 12 steps.
44:
44: Maximum force: 3.36401e-04
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.1-Raspbian-2020.1-1
44:
44: Diagonalizing to find vectors 7 through 18...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--18 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 6 Atoms
44: Using begin = 7 and end = 18
44: Full matrix storage format, nrow=18, ncols=18
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (4257 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Number of degrees of freedom in T-Coupling group System is 6.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=3), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation '1 TIP5P'
44: 6 steps.
44:
44: Maximum force: 2.42882e-04
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.1-Raspbian-2020.1-1
44:
44: Diagonalizing to find vectors 7 through 9...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--9 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 3 Atoms
44: There are: 2 VSites
44: Using begin = 7 and end = 9
44: Full matrix storage format, nrow=9, ncols=9
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (4125 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44: Generated 6 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SW'
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Number of degrees of freedom in T-Coupling group System is 15.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=6), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation 'sw dimer'
44: 12 steps.
44:
44: Maximum force: 1.07599e-03
44: The force is probably not small enough to ensure that you are at a minimum.
44: Be aware that negative eigenvalues may occur
44: when the resulting matrix is diagonalized.
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.1-Raspbian-2020.1-1
44:
44: Diagonalizing to find vectors 7 through 18...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--18 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 6 Atoms
44: There are: 2 Shells
44: There are: 2 VSites
44:
44: NOTE: in the current version shell prediction during the crun is disabled
44:
44: Using begin = 7 and end = 18
44: Full matrix storage format, nrow=18, ncols=18
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (85 ms)
44: [----------] 5 tests from NormalModesWorks/NormalModesTest (29102 ms total)
44:
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.697 0.349 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.214 5.695
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
44:
44: trr version: GMX_trn_file (double precision)
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.8
44: (ns/day) (hour/ns)
44: Performance: 355.446 0.068
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (411 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.562 0.281 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.225 4.593
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.2
44: (ns/day) (hour/ns)
44: Performance: 379.230 0.063
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (345 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.535 0.268 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.485 4.375
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.2
44: (ns/day) (hour/ns)
44: Performance: 378.090 0.063
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (334 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.447 0.224 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.561 3.658
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.007 0.004 194.4
44: (ns/day) (hour/ns)
44: Performance: 384.797 0.062
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (288 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.721 0.361 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.073 5.892
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.5
44: (ns/day) (hour/ns)
44: Performance: 345.868 0.069
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (4493 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.645 0.323 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.551 5.273
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.3
44: (ns/day) (hour/ns)
44: Performance: 344.494 0.070
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (4478 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.523 0.262 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.613 4.276
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.6
44: (ns/day) (hour/ns)
44: Performance: 344.668 0.070
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (4400 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.706 0.353 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.156 5.775
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.5
44: (ns/day) (hour/ns)
44: Performance: 341.818 0.070
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (4489 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.665 0.333 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.415 5.436
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 195.5
44: (ns/day) (hour/ns)
44: Performance: 200.821 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (517 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.739 0.370 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.971 6.043
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 195.4
44: (ns/day) (hour/ns)
44: Performance: 199.185 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (555 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.614 0.308 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.777 5.025
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.007 195.6
44: (ns/day) (hour/ns)
44: Performance: 196.648 0.122
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (641 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.696 0.348 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.218 5.690
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 195.7
44: (ns/day) (hour/ns)
44: Performance: 194.463 0.123
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (631 ms)
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (21584 ms total)
44:
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.874 0.438 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.356 7.152
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.020 0.011 189.7
44: (ns/day) (hour/ns)
44: Performance: 139.785 0.172
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (639 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.826 0.413 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.553 6.754
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.020 0.011 190.3
44: (ns/day) (hour/ns)
44: Performance: 138.643 0.173
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (611 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.977 0.489 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.004 7.990
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.021 0.011 183.1
44: (ns/day) (hour/ns)
44: Performance: 130.435 0.184
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (712 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.765 0.383 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.834 6.260
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 182.1
44: (ns/day) (hour/ns)
44: Performance: 144.269 0.166
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (617 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.709 0.355 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.139 5.798
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 188.3
44: (ns/day) (hour/ns)
44: Performance: 147.992 0.162
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (545 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.029 0.515 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.854 8.410
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.010 187.7
44: (ns/day) (hour/ns)
44: Performance: 150.460 0.160
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (716 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.003 0.502 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.926 8.201
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 188.6
44: (ns/day) (hour/ns)
44: Performance: 143.223 0.168
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (698 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.248 0.624 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.352 10.202
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.010 189.0
44: (ns/day) (hour/ns)
44: Performance: 151.567 0.158
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (820 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 2.051 1.026 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.432 16.766
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 187.3
44: (ns/day) (hour/ns)
44: Performance: 157.431 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (1220 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.133 0.567 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.592 9.261
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 187.4
44: (ns/day) (hour/ns)
44: Performance: 158.061 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (755 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.243 0.622 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.362 10.161
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.5
44: (ns/day) (hour/ns)
44: Performance: 158.325 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (810 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.093 0.546 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.688 8.929
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.029 0.015 192.5
44: (ns/day) (hour/ns)
44: Performance: 96.513 0.249
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (749 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.178 0.589 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.493 9.627
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 189.3
44: (ns/day) (hour/ns)
44: Performance: 147.450 0.163
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (788 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.975 0.488 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.011 7.971
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 189.2
44: (ns/day) (hour/ns)
44: Performance: 148.273 0.162
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (677 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.110 0.555 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.646 9.071
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.020 0.011 187.4
44: (ns/day) (hour/ns)
44: Performance: 138.506 0.173
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (748 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.859 0.930 200.0
44: (ns/day) (hour/ns)
44: Performance: 1.579 15.195
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 189.1
44: (ns/day) (hour/ns)
44: Performance: 146.859 0.163
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (1130 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.819 0.910 200.0
44: (ns/day) (hour/ns)
44: Performance: 1.615 14.861
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 188.8
44: (ns/day) (hour/ns)
44: Performance: 149.627 0.160
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (1102 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.803 0.402 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.655 6.567
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 188.9
44: (ns/day) (hour/ns)
44: Performance: 147.910 0.162
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (597 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.043 0.522 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.815 8.525
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.1
44: (ns/day) (hour/ns)
44: Performance: 157.834 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (720 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.125 0.562 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.611 9.191
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.020 0.011 188.9
44: (ns/day) (hour/ns)
44: Performance: 135.968 0.177
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (762 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.018 0.509 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.885 8.318
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.023 0.012 189.4
44: (ns/day) (hour/ns)
44: Performance: 118.498 0.203
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (713 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 6.322 3.161 200.0
44: (ns/day) (hour/ns)
44: Performance: 0.465 51.653
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.3
44: (ns/day) (hour/ns)
44: Performance: 157.746 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (3370 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.923 0.462 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.179 7.549
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 191.2
44: (ns/day) (hour/ns)
44: Performance: 149.973 0.160
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (783 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.786 0.394 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.732 6.431
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.020 0.010 191.2
44: (ns/day) (hour/ns)
44: Performance: 140.473 0.171
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (717 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.953 0.477 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.080 7.793
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.020 0.011 189.3
44: (ns/day) (hour/ns)
44: Performance: 139.216 0.172
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (797 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.823 0.412 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.565 6.732
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 189.6
44: (ns/day) (hour/ns)
44: Performance: 148.763 0.161
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (728 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 2.209 1.105 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.329 18.058
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.8
44: (ns/day) (hour/ns)
44: Performance: 154.711 0.155
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (1403 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.006 0.504 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.916 8.230
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.010 189.0
44: (ns/day) (hour/ns)
44: Performance: 151.971 0.158
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (803 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.844 0.922 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.593 15.070
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.5
44: (ns/day) (hour/ns)
44: Performance: 156.898 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (1219 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.251 0.626 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.347 10.226
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.8
44: (ns/day) (hour/ns)
44: Performance: 155.284 0.155
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (922 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.028 0.515 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.854 8.408
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.7
44: (ns/day) (hour/ns)
44: Performance: 156.146 0.154
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (811 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.762 0.381 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.852 6.231
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.7
44: (ns/day) (hour/ns)
44: Performance: 156.456 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (678 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.562 0.782 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.879 12.772
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 187.3
44: (ns/day) (hour/ns)
44: Performance: 156.790 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (1078 ms)
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (29444 ms total)
44:
44: [----------] 2 tests from Angles1/SimpleMdrunTest
44: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Excluding 3 bonded neighbours molecule type 'butane'
44:
44: NOTE 2 [file angles1.top, line 72]:
44: In moleculetype 'butane' 4 atoms are not bound by a potential or
44: constraint to any other atom in the same moleculetype. Although
44: technically this might not cause issues in a simulation, this often means
44: that the user forgot to add a bond/potential/constraint or put multiple
44: molecules in the same moleculetype definition by mistake. Run with -v to
44: get information for each atom.
44:
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 238.919 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'This_incredible_box_of_butane'
44: 50 steps, 0.1 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
44: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 2.390 1.195 200.0
44: (ns/day) (hour/ns)
44: Performance: 3.687 6.509
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
44: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (1270 ms)
44: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Excluding 3 bonded neighbours molecule type 'butane'
44:
44: NOTE 2 [file angles1.top, line 72]:
44: In moleculetype 'butane' 4 atoms are not bound by a potential or
44: constraint to any other atom in the same moleculetype. Although
44: technically this might not cause issues in a simulation, this often means
44: that the user forgot to add a bond/potential/constraint or put multiple
44: molecules in the same moleculetype definition by mistake. Run with -v to
44: get information for each atom.
44:
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 238.919 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'This_incredible_box_of_butane'
44: 50 steps, 0.1 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
44: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.667 0.334 199.9
44: (ns/day) (hour/ns)
44: Performance: 13.212 1.817
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
44: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (386 ms)
44: [----------] 2 tests from Angles1/SimpleMdrunTest (1658 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 65 tests from 7 test cases ran. (96346 ms total)
44: [ PASSED ] 65 tests.
44/52 Test #44: MdrunNonIntegratorTests ............. Passed 96.53 sec
test 45
Start 45: MdrunTpiTests
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 2 tests from 1 test case.
45: [----------] Global test environment set-up.
45: [----------] 2 tests from Simple/TpiTest
45: [ RUN ] Simple/TpiTest.ReproducesOutput/0
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45: Using 1 OpenMP thread
45:
45:
45: NOTE: Thread affinity was not set.
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/0 (4645 ms)
45: [ RUN ] Simple/TpiTest.ReproducesOutput/1
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45: Using 1 OpenMP thread
45:
45:
45: NOTE: Thread affinity was not set.
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/1 (4670 ms)
45: [----------] 2 tests from Simple/TpiTest (9315 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 2 tests from 1 test case ran. (9316 ms total)
45: [ PASSED ] 2 tests.
45/52 Test #45: MdrunTpiTests ....................... Passed 9.39 sec
test 46
Start 46: MdrunMpiTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 22 tests from 7 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from DomainDecompositionSpecialCasesTest
46: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -1266872078
46: Generated 3 of the 3 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 3 of the 3 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 9.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.006 0.002 302.3
46: (ns/day) (hour/ns)
46: Performance: 45.994 0.522
46: This run will generate roughly 0 Mb of data
46: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (90 ms)
46: [----------] 1 test from DomainDecompositionSpecialCasesTest (91 ms total)
46:
46: [----------] 4 tests from MimicTest
46: [ RUN ] MimicTest.OneQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -400138845
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.548 0.667 382.0
46: (ns/day) (hour/ns)
46: Performance: 0.130 185.269
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.OneQuantumMol (2058 ms)
46: [ RUN ] MimicTest.AllQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 935349804
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.590 0.677 382.3
46: (ns/day) (hour/ns)
46: Performance: 0.128 188.163
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.AllQuantumMol (2081 ms)
46: [ RUN ] MimicTest.TwoQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 1998603347
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.610 0.682 382.4
46: (ns/day) (hour/ns)
46: Performance: 0.127 189.551
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.TwoQuantumMol (2094 ms)
46: [ RUN ] MimicTest.BondCuts
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -1564145313
46: Generated 2211 of the 2211 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2211 of the 2211 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
46: Number of degrees of freedom in T-Coupling group rest is 66.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: NVE simulation: will use the initial temperature of 300.368 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
46:
46: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.549 0.667 382.0
46: (ns/day) (hour/ns)
46: Performance: 0.129 185.358
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
46: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.BondCuts (2157 ms)
46: [----------] 4 tests from MimicTest (8394 ms total)
46:
46: [----------] 1 test from MultiSimTerminationTest
46: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
46: [----------] 1 test from MultiSimTerminationTest (0 ms total)
46:
46: [----------] 3 tests from PmeTest
46: [ RUN ] PmeTest.ReproducesEnergies
46: Setting the LD random seed to 723973525
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 9.282 2.360 393.3
46: (ns/day) (hour/ns)
46: Performance: 0.769 31.216
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 9.562 2.430 393.5
46: (ns/day) (hour/ns)
46: Performance: 0.747 32.140
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 9.818 2.495 393.5
46: (ns/day) (hour/ns)
46: Performance: 0.727 32.998
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10277 ms)
46: [ RUN ] PmeTest.ScalesTheBox
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -1521560828
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.411 0.140 293.9
46: (ns/day) (hour/ns)
46: Performance: 0.618 38.818
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBox (1085 ms)
46: [ RUN ] PmeTest.ScalesTheBoxWithWalls
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 356930297
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Searching the wall atom type(s)
46: Number of degrees of freedom in T-Coupling group rest is 13.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: NVE simulation: will use the initial temperature of 966.268 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.831 0.247 335.9
46: (ns/day) (hour/ns)
46: Performance: 0.349 68.690
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBoxWithWalls (1379 ms)
46: [----------] 3 tests from PmeTest (12742 ms total)
46:
46: [----------] 1 test from ReplicaExchangeTerminationTest
46: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
46: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.79910463671071e+01
46: Maximum force = 1.86297359432218e+02 on atom 13
46: Norm of force = 8.77219865482161e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (7260 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.58622538633290e+01
46: Maximum force = 4.27274822366538e+02 on atom 13
46: Norm of force = 1.84530029253833e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (8789 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19376899751521e+02
46: Maximum force = 9.99884921009767e+03 on atom 9
46: Norm of force = 4.61669565054298e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4306 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.51743018140926e+02
46: Maximum force = 7.42089573409112e+03 on atom 9
46: Norm of force = 3.56929298615739e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5816 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.56984193848276e+02
46: Maximum force = 4.56923624626296e+02 on atom 17
46: Norm of force = 1.83258377168331e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4767 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06800e+03 on atom 28
46: F-Norm = 4.26922e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.69410778678185e+02
46: Maximum force = 2.18225948474048e+02 on atom 17
46: Norm of force = 7.92068036537643e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7120 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (38060 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.74257075835450e-01
46: Maximum force = 4.01322929015108e+00 on atom 3
46: Norm of force = 1.63839399694368e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1645 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 3
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 3
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2113 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19395484891518e+02
46: Maximum force = 9.97041707197910e+03 on atom 9
46: Norm of force = 4.62274878665467e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3899 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.56258793899479e+02
46: Maximum force = 7.50181017480397e+03 on atom 9
46: Norm of force = 3.61390332564874e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5435 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1066 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (14182 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 22 tests from 7 test cases ran. (73473 ms total)
46: [ PASSED ] 22 tests.
46:
46: YOU HAVE 4 DISABLED TESTS
46:
46/52 Test #46: MdrunMpiTests ....................... Passed 73.57 sec
test 47
Start 47: MdrunMpiCoordinationTestsOneRank
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
47: Test timeout computed to be: 480
47: [==========] Running 27 tests from 3 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest
47: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.347 0.348 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.227 5.678
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.358 0.358 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.098 5.857
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.268 0.269 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.458 4.397
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.324 0.325 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.520 5.309
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.301 0.302 99.7
47: (ns/day) (hour/ns)
47: Performance: 4.859 4.939
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.335 0.336 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.377 5.483
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2516 ms)
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest (2516 ms total)
47:
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.284 0.284 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.164 4.648
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.302 0.303 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.848 4.950
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.281 0.281 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.221 4.597
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.324 0.325 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.523 5.307
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.287 0.288 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.099 4.707
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.298 0.299 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.918 4.880
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2011 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.328 0.328 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.472 5.367
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.358 0.358 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.100 5.853
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.314 0.315 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.668 5.142
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.359 0.360 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.085 5.875
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.411 0.412 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.564 6.733
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.372 0.373 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.943 6.087
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2401 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.422 0.422 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.477 6.902
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.420 0.421 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.489 6.879
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.414 0.415 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.541 6.777
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.469 0.470 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.127 7.675
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.279 0.280 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.252 4.570
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.313 0.313 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.688 5.119
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2576 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.349 0.349 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.208 5.704
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.280 0.280 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.244 4.576
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.252 0.253 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.809 4.132
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.329 0.330 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.454 5.389
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.273 0.274 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.361 4.477
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.286 0.287 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.123 4.685
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2039 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.375 0.376 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.911 6.136
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.489 0.489 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.002 7.994
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.345 0.346 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.247 5.650
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.332 0.333 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.417 5.434
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.342 0.342 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.290 5.595
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.007 1.007 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.458 16.458
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3290 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.207 1.207 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.217 19.719
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.465 0.466 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.155 7.607
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.320 0.320 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.584 5.235
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.290 0.291 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.045 4.757
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.400 0.401 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.663 6.551
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.369 0.370 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.970 6.046
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3370 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.347 0.347 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.232 5.671
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.369 0.370 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.974 6.039
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.787 0.788 99.9
47: (ns/day) (hour/ns)
47: Performance: 1.864 12.876
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.338 0.339 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.335 5.536
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.644 0.644 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.280 10.525
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.127 1.128 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.303 18.425
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4363 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.793 0.793 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.852 12.961
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.482 0.483 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.044 7.885
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.492 0.493 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.982 8.048
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.516 0.517 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.843 8.441
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.421 0.422 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.483 6.890
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.479 0.479 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.064 7.833
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3636 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.596 0.596 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.465 9.738
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.473 0.473 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.106 7.727
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.294 0.294 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.993 4.807
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.602 0.602 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.440 9.838
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.578 0.579 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.536 9.463
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.706 0.707 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.077 11.553
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3602 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.255 0.255 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.759 4.168
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.333 0.334 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.402 5.452
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.283 0.284 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.180 4.633
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.316 0.316 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.642 5.170
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.282 0.282 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.200 4.616
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.359 0.360 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.082 5.879
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2063 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.307 0.307 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.786 5.015
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.299 0.299 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.905 4.893
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.829 1.830 100.0
47: (ns/day) (hour/ns)
47: Performance: 0.803 29.903
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.288 0.289 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.079 4.725
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.325 0.326 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.512 5.320
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.441 0.442 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.323 7.222
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (3924 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.382 0.382 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.845 6.242
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.277 0.277 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.297 4.531
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.271 0.271 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.413 4.434
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.279 0.279 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.260 4.563
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.512 0.513 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.863 8.382
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.320 0.321 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.579 5.241
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2276 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.262 0.262 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.599 4.287
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.258 0.258 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.694 4.215
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.271 0.271 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.420 4.428
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.276 0.277 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.310 4.519
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.304 0.304 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.825 4.974
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.329 0.329 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.467 5.373
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1923 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.325 0.325 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.522 5.308
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.421 0.422 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.483 6.890
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.405 0.405 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.624 6.623
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.701 0.702 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.093 11.466
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.017 1.018 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.444 16.626
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.389 1.390 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.057 22.707
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (4856 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.389 0.389 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.771 6.364
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.454 0.454 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.234 7.421
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.645 0.645 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.277 10.538
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.361 0.361 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.065 5.904
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.629 0.629 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.334 10.283
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.395 0.395 100.0
47: (ns/day) (hour/ns)
47: Performance: 3.715 6.460
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (3421 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.491 0.491 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.990 8.028
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.377 0.377 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.896 6.160
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.734 0.735 99.9
47: (ns/day) (hour/ns)
47: Performance: 1.999 12.005
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.811 0.812 99.9
47: (ns/day) (hour/ns)
47: Performance: 1.809 13.269
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.429 0.430 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.416 7.026
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.473 0.474 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.100 7.742
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (4016 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.422 0.422 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.479 6.898
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.465 0.465 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.156 7.604
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.306 0.307 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.790 5.010
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.322 0.322 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.560 5.263
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.325 0.326 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.509 5.322
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.402 0.403 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.646 6.583
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (2592 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.351 0.351 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.180 5.742
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.513 0.514 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.860 8.392
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.482 0.483 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.041 7.893
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.348 0.348 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.217 5.692
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.336 0.337 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.365 5.499
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.317 0.317 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.633 5.180
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (2645 ms)
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (55011 ms total)
47:
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.472 0.472 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.113 7.710
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.197 1.197 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.227 19.566
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.365 0.365 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.021 5.969
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.434 0.434 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.382 7.097
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.368 0.368 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.989 6.017
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.317 0.317 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.626 5.188
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (28101 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.430 0.430 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.414 7.030
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.319 0.319 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.599 5.218
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.333 0.334 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.399 5.455
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.324 0.324 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.532 5.295
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.375 0.376 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.911 6.136
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.437 0.437 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.357 7.148
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (27078 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.448 0.448 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.280 7.318
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.285 0.286 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.144 4.665
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.366 0.367 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.004 5.994
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.347 0.347 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.232 5.671
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.278 0.279 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.273 4.551
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.295 0.296 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.970 4.829
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (26810 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.381 0.382 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.847 6.238
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.853 0.854 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.720 13.950
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.394 0.395 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.722 6.448
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.331 0.331 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.433 5.414
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.675 0.675 99.9
47: (ns/day) (hour/ns)
47: Performance: 2.175 11.037
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.346 0.347 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.234 5.668
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (27776 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.356 0.356 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.127 5.816
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.328 0.328 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.477 5.361
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.481 0.482 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.047 7.876
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.308 0.309 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.754 5.048
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.377 0.377 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.891 6.168
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.295 0.296 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.967 4.832
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (27690 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.429 0.430 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.419 7.020
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.322 0.323 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.553 5.271
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.389 0.389 99.8
47: (ns/day) (hour/ns)
47: Performance: 3.774 6.359
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.362 0.363 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.051 5.924
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.309 0.310 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.740 5.063
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.389 0.390 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.771 6.365
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (27366 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.252 0.252 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.821 4.123
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.268 0.268 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.475 4.384
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.367 0.367 100.0
47: (ns/day) (hour/ns)
47: Performance: 4.004 5.995
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.319 0.319 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.602 5.215
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.255 0.255 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.751 4.173
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.287 0.287 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.117 4.690
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (26534 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.503 0.504 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.917 8.228
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.323 0.323 100.0
47: (ns/day) (hour/ns)
47: Performance: 4.548 5.277
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.551 0.551 100.0
47: (ns/day) (hour/ns)
47: Performance: 2.663 9.011
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.281 0.281 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.223 4.595
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.270 0.270 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.431 4.419
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.320 0.321 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.580 5.240
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (27045 ms)
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (218402 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 27 tests from 3 test cases ran. (275929 ms total)
47: [ PASSED ] 27 tests.
47/52 Test #47: MdrunMpiCoordinationTestsOneRank .... Passed 276.02 sec
test 48
Start 48: MdrunMpiCoordinationTestsTwoRanks
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
48: Test timeout computed to be: 480
48: [==========] Running 27 tests from 3 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest
48: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.570 0.285 199.8
48: (ns/day) (hour/ns)
48: Performance: 5.151 4.660
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.684 0.343 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.284 5.602
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.598 0.300 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.901 4.897
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.663 0.332 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.421 5.428
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.652 0.327 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.497 5.337
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.706 0.354 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.153 5.780
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2289 ms)
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest (2290 ms total)
48:
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.616 0.308 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.765 5.037
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.565 0.283 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.187 4.627
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.621 0.311 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.725 5.079
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.495 0.248 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.922 4.053
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.566 0.284 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.179 4.634
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.624 0.312 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.700 5.106
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2022 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.673 0.337 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.361 5.503
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.752 0.377 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.901 6.153
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.680 0.341 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.311 5.567
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.648 0.325 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.523 5.306
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.779 0.390 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.763 6.378
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.620 0.311 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.728 5.076
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2383 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.749 0.375 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.917 6.127
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.672 0.337 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.361 5.504
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.812 0.407 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.609 6.650
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.589 0.296 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.970 4.829
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.709 0.355 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.136 5.803
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.589 0.295 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.977 4.822
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2455 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.551 0.276 199.8
48: (ns/day) (hour/ns)
48: Performance: 5.327 4.506
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.520 0.261 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.635 4.259
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.617 0.309 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.746 5.057
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.600 0.301 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.884 4.914
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.874 0.438 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.354 7.155
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.518 1.260 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.166 20.589
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3415 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 3.750 1.875 200.0
48: (ns/day) (hour/ns)
48: Performance: 0.783 30.642
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.938 0.470 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.128 7.673
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.619 0.311 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.730 5.074
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.617 0.309 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.747 5.056
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.644 0.323 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.551 5.273
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.625 0.313 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.689 5.118
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4000 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.675 0.338 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.346 5.523
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.638 0.319 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.598 5.220
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.627 0.315 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.670 5.139
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.562 0.282 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.205 4.611
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.839 0.920 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.596 15.036
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.005 0.503 199.6
48: (ns/day) (hour/ns)
48: Performance: 2.918 8.224
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2933 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.633 0.317 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.633 5.180
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.597 0.299 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.916 4.882
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.672 0.337 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.364 5.500
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.736 0.369 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.984 6.024
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.977 0.489 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.003 7.993
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.792 0.397 199.5
48: (ns/day) (hour/ns)
48: Performance: 3.701 6.484
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2549 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.373 0.687 199.9
48: (ns/day) (hour/ns)
48: Performance: 2.139 11.222
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.696 0.348 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.216 5.692
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.683 0.342 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.296 5.587
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.839 0.920 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.596 15.035
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.775 0.388 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.784 6.342
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.750 0.376 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.910 6.138
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3330 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.640 0.321 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.582 5.238
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.650 0.325 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.514 5.317
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.703 0.852 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.723 13.925
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.632 0.816 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.799 13.340
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.867 0.434 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.383 7.095
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.658 0.330 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.453 5.390
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3581 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.885 0.443 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.316 7.237
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.520 0.261 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.635 4.259
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.662 0.332 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.424 5.425
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.604 0.303 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.853 4.946
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.667 0.335 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.388 5.469
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.677 0.339 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.328 5.546
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2337 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.632 0.316 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.643 5.169
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.750 0.376 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.910 6.139
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.654 0.328 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.483 5.354
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.772 0.387 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.799 6.317
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.778 0.390 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.768 6.369
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.312 0.656 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.238 10.725
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2702 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.619 0.310 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.742 5.061
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.803 0.402 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.656 6.565
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.863 0.432 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.399 7.061
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.126 0.563 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.607 9.206
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.777 0.390 199.5
48: (ns/day) (hour/ns)
48: Performance: 3.770 6.366
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.774 0.388 199.5
48: (ns/day) (hour/ns)
48: Performance: 3.785 6.341
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2754 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.588 0.295 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.984 4.815
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.573 0.788 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.865 12.869
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.436 0.719 199.7
48: (ns/day) (hour/ns)
48: Performance: 2.043 11.746
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.597 0.300 199.3
48: (ns/day) (hour/ns)
48: Performance: 4.901 4.897
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.557 0.279 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.256 4.566
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.622 0.312 199.3
48: (ns/day) (hour/ns)
48: Performance: 4.703 5.103
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3124 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.616 0.309 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.761 5.041
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.602 0.802 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.832 13.099
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.707 0.354 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.147 5.787
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.953 0.477 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.078 7.797
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.927 0.464 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.164 7.587
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.810 0.906 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.622 14.800
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (3607 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.027 0.514 199.7
48: (ns/day) (hour/ns)
48: Performance: 2.857 8.401
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.560 0.281 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.225 4.594
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.366 0.684 199.7
48: (ns/day) (hour/ns)
48: Performance: 2.147 11.179
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.619 0.311 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.729 5.075
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 3.484 1.743 199.9
48: (ns/day) (hour/ns)
48: Performance: 0.843 28.481
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.584 0.793 199.7
48: (ns/day) (hour/ns)
48: Performance: 1.852 12.962
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (4826 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.820 0.410 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.578 6.707
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.736 0.368 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.987 6.019
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.861 0.431 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.407 7.045
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.604 0.303 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.850 4.948
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.368 0.685 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.146 11.186
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.611 0.306 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.799 5.001
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (3368 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.631 0.316 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.650 5.161
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.561 0.281 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.225 4.593
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.306 0.654 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.247 10.682
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.570 0.285 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.146 4.664
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.553 0.277 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.306 4.523
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.030 0.516 199.7
48: (ns/day) (hour/ns)
48: Performance: 2.849 8.424
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (2760 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.022 0.511 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.873 8.355
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.757 0.379 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.876 6.193
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.688 0.345 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.260 5.634
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.714 0.358 199.5
48: (ns/day) (hour/ns)
48: Performance: 4.103 5.849
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.593 0.297 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.948 4.851
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.686 0.343 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.277 5.612
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (2625 ms)
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (54780 ms total)
48:
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.729 0.365 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.024 5.964
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.643 0.322 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.561 5.262
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.841 0.421 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.490 6.877
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.925 0.463 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.170 7.570
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.296 0.648 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.265 10.596
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.773 0.387 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.793 6.327
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (27776 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.965 0.483 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.040 7.895
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.827 0.414 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.547 6.766
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.825 0.413 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.554 6.754
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.725 0.363 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.045 5.934
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.936 0.469 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.133 7.660
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 3.528 1.765 199.9
48: (ns/day) (hour/ns)
48: Performance: 0.832 28.832
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (29091 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.710 0.356 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.131 5.810
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.644 0.322 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.556 5.268
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.643 0.322 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.557 5.267
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.908 0.455 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.231 7.428
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.730 0.365 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.019 5.971
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.626 0.313 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.685 5.122
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (27241 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.493 1.247 199.9
48: (ns/day) (hour/ns)
48: Performance: 1.178 20.372
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.713 0.357 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.115 5.833
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.676 0.339 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.337 5.534
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.821 0.411 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.574 6.715
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.707 0.354 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.148 5.785
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.856 0.429 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.426 7.006
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (28212 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.888 0.444 199.8
48: (ns/day) (hour/ns)
48: Performance: 3.306 7.260
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.755 0.378 199.7
48: (ns/day) (hour/ns)
48: Performance: 3.888 6.173
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.577 0.289 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.084 4.720
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.643 0.322 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.559 5.264
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.719 0.360 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.077 5.887
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.691 0.346 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.244 5.655
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (27311 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.656 0.329 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.471 5.368
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.714 0.358 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.107 5.844
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.781 0.391 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.754 6.393
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.590 0.296 199.3
48: (ns/day) (hour/ns)
48: Performance: 4.957 4.841
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.704 0.353 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.165 5.762
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.651 0.326 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.506 5.327
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (27889 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.804 0.404 199.3
48: (ns/day) (hour/ns)
48: Performance: 3.640 6.593
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.703 0.352 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.167 5.759
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.835 0.418 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.510 6.838
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.302 1.152 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.275 18.826
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.609 0.306 199.1
48: (ns/day) (hour/ns)
48: Performance: 4.806 4.993
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.576 0.289 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.087 4.718
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (28489 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.840 0.421 199.6
48: (ns/day) (hour/ns)
48: Performance: 3.492 6.874
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.775 0.389 199.3
48: (ns/day) (hour/ns)
48: Performance: 3.777 6.355
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.617 0.310 199.0
48: (ns/day) (hour/ns)
48: Performance: 4.739 5.064
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.657 0.330 199.0
48: (ns/day) (hour/ns)
48: Performance: 4.449 5.395
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.766 0.384 199.4
48: (ns/day) (hour/ns)
48: Performance: 3.824 6.275
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.617 0.310 199.3
48: (ns/day) (hour/ns)
48: Performance: 4.743 5.060
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (27433 ms)
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (223443 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 27 tests from 3 test cases ran. (280514 ms total)
48: [ PASSED ] 27 tests.
48/52 Test #48: MdrunMpiCoordinationTestsTwoRanks ... Passed 280.61 sec
test 49
Start 49: GmxapiExternalInterfaceTests
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
49: Test timeout computed to be: 600
49: [==========] Running 9 tests from 2 test cases.
49: [----------] Global test environment set-up.
49: [----------] 8 tests from GmxApiTest
49: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
49: Setting the LD random seed to -57742937
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.484 0.371 399.7
49: (ns/day) (hour/ns)
49: Performance: 1.363 17.605
49: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (4555 ms)
49: [ RUN ] GmxApiTest.SystemConstruction
49: Setting the LD random seed to 1577707788
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49: [ OK ] GmxApiTest.SystemConstruction (4149 ms)
49: [ RUN ] GmxApiTest.SaneVersionComparisons
49: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
49: [ RUN ] GmxApiTest.VersionNamed0_1_Features
49: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
49: [ RUN ] GmxApiTest.RunnerBasicMD
49: Setting the LD random seed to -1080418965
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.558 0.390 399.7
49: (ns/day) (hour/ns)
49: Performance: 1.299 18.474
49: [ OK ] GmxApiTest.RunnerBasicMD (4522 ms)
49: [ RUN ] GmxApiTest.RunnerReinitialize
49: Setting the LD random seed to 1077204114
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49:
49: Received the remote INT/TERM signal, stopping within 50 steps
49:
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.614 0.404 399.6
49: (ns/day) (hour/ns)
49: Performance: 8.772 2.736
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.759 0.441 399.3
49: (ns/day) (hour/ns)
49: Performance: 8.044 2.983
49: [ OK ] GmxApiTest.RunnerReinitialize (5018 ms)
49: [ RUN ] GmxApiTest.RunnerContinuedMD
49: Setting the LD random seed to -1418709442
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 10 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 2.390 0.598 399.7
49: (ns/day) (hour/ns)
49: Performance: 3.104 7.732
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.453 0.364 399.2
49: (ns/day) (hour/ns)
49: Performance: 9.738 2.465
49: [ OK ] GmxApiTest.RunnerContinuedMD (5120 ms)
49: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
49: Setting the LD random seed to 2059722616
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 1 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.746 0.437 399.7
49: (ns/day) (hour/ns)
49: Performance: 0.773 31.056
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
49:
49: NOTE: Parallelization is limited by the small number of atoms,
49: only starting 1 thread-MPI ranks.
49: You can use the -nt and/or -ntmpi option to optimize the number of threads.
49:
49: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49:
49: Using 1 MPI thread
49: Using 4 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.372 0.343 399.5
49: (ns/day) (hour/ns)
49: Performance: 0.983 24.415
49: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4942 ms)
49: [----------] 8 tests from GmxApiTest (28317 ms total)
49:
49: [----------] 1 test from GmxApiBasicTest
49: [ RUN ] GmxApiBasicTest.Status
49: [ OK ] GmxApiBasicTest.Status (0 ms)
49: [----------] 1 test from GmxApiBasicTest (0 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 9 tests from 2 test cases ran. (28318 ms total)
49: [ PASSED ] 9 tests.
49/52 Test #49: GmxapiExternalInterfaceTests ........ Passed 28.40 sec
test 50
Start 50: GmxapiMpiTests
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiMpiTests.xml"
50: Test timeout computed to be: 600
50: [==========] Running 9 tests from 2 test cases.
50: [----------] Global test environment set-up.
50: [----------] 8 tests from GmxApiTest
50: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
50: Setting the LD random seed to 1142136084
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.871 0.468 399.8
50: (ns/day) (hour/ns)
50: Performance: 1.082 22.190
50: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (4611 ms)
50: [ RUN ] GmxApiTest.SystemConstruction
50: Setting the LD random seed to -1274345255
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50: [ OK ] GmxApiTest.SystemConstruction (4163 ms)
50: [ RUN ] GmxApiTest.SaneVersionComparisons
50: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
50: [ RUN ] GmxApiTest.VersionNamed0_1_Features
50: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
50: [ RUN ] GmxApiTest.RunnerBasicMD
50: Setting the LD random seed to -493907695
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.649 0.412 399.7
50: (ns/day) (hour/ns)
50: Performance: 1.227 19.552
50: [ OK ] GmxApiTest.RunnerBasicMD (4551 ms)
50: [ RUN ] GmxApiTest.RunnerReinitialize
50: Setting the LD random seed to 422561433
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50:
50: Received the remote INT/TERM signal, stopping within 50 steps
50:
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.973 0.494 399.6
50: (ns/day) (hour/ns)
50: Performance: 7.178 3.344
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.988 0.498 399.4
50: (ns/day) (hour/ns)
50: Performance: 7.120 3.371
50: [ OK ] GmxApiTest.RunnerReinitialize (5144 ms)
50: [ RUN ] GmxApiTest.RunnerContinuedMD
50: Setting the LD random seed to -1357991188
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 10 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.253 0.314 399.5
50: (ns/day) (hour/ns)
50: Performance: 5.917 4.056
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.320 0.331 399.3
50: (ns/day) (hour/ns)
50: Performance: 10.719 2.239
50: [ OK ] GmxApiTest.RunnerContinuedMD (4800 ms)
50: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
50: Setting the LD random seed to 456972527
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 1 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.415 0.354 399.6
50: (ns/day) (hour/ns)
50: Performance: 0.953 25.184
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.1-Raspbian-2020.1-1 (double precision)
50:
50: NOTE: Parallelization is limited by the small number of atoms,
50: only starting 1 thread-MPI ranks.
50: You can use the -nt and/or -ntmpi option to optimize the number of threads.
50:
50: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50:
50: Using 1 MPI thread
50: Using 4 OpenMP threads
50:
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.098 0.275 399.4
50: (ns/day) (hour/ns)
50: Performance: 1.228 19.551
50: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4787 ms)
50: [----------] 8 tests from GmxApiTest (28062 ms total)
50:
50: [----------] 1 test from GmxApiBasicTest
50: [ RUN ] GmxApiBasicTest.Status
50: [ OK ] GmxApiBasicTest.Status (0 ms)
50: [----------] 1 test from GmxApiBasicTest (0 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 9 tests from 2 test cases ran. (28062 ms total)
50: [ PASSED ] 9 tests.
50/52 Test #50: GmxapiMpiTests ...................... Passed 28.14 sec
test 51
Start 51: GmxapiInternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 2 tests from 1 test case.
51: [----------] Global test environment set-up.
51: [----------] 2 tests from GmxApiTest
51: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
51: Setting the LD random seed to 140234166
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.BuildApiWorkflowImpl (4040 ms)
51: [ RUN ] GmxApiTest.CreateApiWorkflow
51: Setting the LD random seed to -115901176
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.CreateApiWorkflow (4119 ms)
51: [----------] 2 tests from GmxApiTest (8159 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 2 tests from 1 test case ran. (8160 ms total)
51: [ PASSED ] 2 tests.
51/52 Test #51: GmxapiInternalInterfaceTests ........ Passed 8.24 sec
test 52
Start 52: GmxapiInternalsMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalsMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 2 tests from 1 test case.
52: [----------] Global test environment set-up.
52: [----------] 2 tests from GmxApiTest
52: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
52: Setting the LD random seed to -1654945284
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.BuildApiWorkflowImpl (4010 ms)
52: [ RUN ] GmxApiTest.CreateApiWorkflow
52: Setting the LD random seed to -343286517
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.CreateApiWorkflow (4149 ms)
52: [----------] 2 tests from GmxApiTest (8161 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 2 tests from 1 test case ran. (8161 ms total)
52: [ PASSED ] 2 tests.
52/52 Test #52: GmxapiInternalsMpiTests ............. Passed 8.24 sec
100% tests passed, 0 tests failed out of 52
Label Time Summary:
GTest = 1024.47 sec*proc (52 tests)
IntegrationTest = 390.73 sec*proc (9 tests)
MpiTest = 667.26 sec*proc (8 tests)
SlowTest = 556.63 sec*proc (2 tests)
UnitTest = 77.11 sec*proc (41 tests)
Total Test time (real) = 1024.91 sec
touch build-basic
dh_testdir
/usr/bin/make -j4 -C build/mpich
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich/CMakeFiles /<<PKGBUILDDIR>>/build/mpich/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.1-Raspbian-2020.1-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=/<<PKGBUILDDIR>>/src:/<<PKGBUILDDIR>>/python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.1-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target scanner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
Scanning dependencies of target thread_mpi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
[ 1%] Built target thread_mpi
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target scanner
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 5%] Built target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 8%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)', declared with attribute warn_unused_result [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)', declared with attribute warn_unused_result [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1293:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1293 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1294 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1295 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1296 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -P CMakeFiles/libgromacs.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libgromacs_mdrun_mpi.mpich.a CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/awh/awh.cpp.o CMakeFiles/libgromacs.dir/awh/bias.cpp.o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/awh/grid.cpp.o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energyelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o
/usr/bin/ranlib ../../lib/libgromacs_mdrun_mpi.mpich.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 98%] Built target libgromacs
/usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun.dir/mdrun_main.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/mdrun_mpi.mpich ../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[100%] Built target mdrun
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -j4 -C build/mpich-dp
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.1-Raspbian-2020.1-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=/<<PKGBUILDDIR>>/src:/<<PKGBUILDDIR>>/python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.1-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target thread_mpi
Scanning dependencies of target scanner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target thread_mpi
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/programs /<<PKGBUILDDIR>>/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target scanner
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In static member function 'static void std::_Function_handler<void(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Functor = gmx::FreeEnergyPerturbationElement::scheduleTask(gmx::Step, gmx::Time, const RegisterRunFunctionPtr&)::<lambda()>; _ArgTypes = {}]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:85:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
85 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:67:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
67 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:85:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
85 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In function 'virtual void gmx::StatePropagatorData::trajectoryWriterTeardown(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/9/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 5%] Built target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 8%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' {aka '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' {aka '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const MPI_Comm*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<edpar> {anonymous}::read_edi_file(const char*, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)', declared with attribute warn_unused_result [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/9/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:356:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
356 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>